data_2BF1 # _entry.id 2BF1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2BF1 PDBE EBI-21845 WWPDB D_1290021845 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2BF1 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2004-12-02 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Chen, B.' 1 ? 'Vogan, E.M.' 2 ? 'Gong, H.' 3 ? 'Skehel, J.J.' 4 ? 'Wiley, D.C.' 5 ? 'Harrison, S.C.' 6 ? # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structure of an Unliganded Simian Immunodeficiency Virus Gp120 Core' Nature 433 834 ? 2005 NATUAS UK 0028-0836 0006 ? 15729334 10.1038/NATURE03327 1 'Determining the Structure of the Unliganded and Fully-Glycosylated Siv Gp120 Envelope Glycoprotein.' Structure 13 197 ? 2005 STRUE6 UK 0969-2126 2005 ? 15698564 10.1016/J.STR.2004.12.004 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, B.' 1 ? primary 'Vogan, E.M.' 2 ? primary 'Gong, H.' 3 ? primary 'Skehel, J.J.' 4 ? primary 'Wiley, D.C.' 5 ? primary 'Harrison, S.C.' 6 ? 1 'Chen, B.' 7 ? 1 'Vogan, E.M.' 8 ? 1 'Gong, H.' 9 ? 1 'Skehel, J.J.' 10 ? 1 'Wiley, D.C.' 11 ? 1 'Harrison, S.C.' 12 ? # _cell.entry_id 2BF1 _cell.length_a 108.048 _cell.length_b 108.048 _cell.length_c 117.701 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BF1 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'EXTERIOR MEMBRANE GLYCOPROTEIN GP120' 36833.723 1 ? ? 'GP120 CORE, RESIDUES 66-109,209-311,342-502' ? 2 branched man ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; 732.682 3 ? ? ? ? 3 branched man ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; 1056.964 2 ? ? ? ? 4 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose' 570.542 2 ? ? ? ? 5 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401 1 ? ? ? ? 6 branched man ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; 1235.105 1 ? ? ? ? 7 branched man ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; 910.823 1 ? ? ? ? 8 branched man ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; 748.682 1 ? ? ? ? 9 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'SIV GP120' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;HMELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCIGAGHCNTSIIQESCDKHYWDTIRFRYCAPPGYAL LRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRGAGWCWFG GNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRR NYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLVEIT ; _entity_poly.pdbx_seq_one_letter_code_can ;HMELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCIGAGHCNTSIIQESCDKHYWDTIRFRYCAPPGYAL LRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRGAGWCWFG GNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRR NYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLVEIT ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 MET n 1 3 GLU n 1 4 LEU n 1 5 ALA n 1 6 LEU n 1 7 ASN n 1 8 VAL n 1 9 THR n 1 10 GLU n 1 11 SER n 1 12 PHE n 1 13 ASP n 1 14 ALA n 1 15 TRP n 1 16 GLU n 1 17 ASN n 1 18 THR n 1 19 VAL n 1 20 THR n 1 21 GLU n 1 22 GLN n 1 23 ALA n 1 24 ILE n 1 25 GLU n 1 26 ASP n 1 27 VAL n 1 28 TRP n 1 29 GLN n 1 30 LEU n 1 31 PHE n 1 32 GLU n 1 33 THR n 1 34 SER n 1 35 ILE n 1 36 LYS n 1 37 PRO n 1 38 CYS n 1 39 VAL n 1 40 LYS n 1 41 LEU n 1 42 SER n 1 43 PRO n 1 44 LEU n 1 45 CYS n 1 46 ILE n 1 47 GLY n 1 48 ALA n 1 49 GLY n 1 50 HIS n 1 51 CYS n 1 52 ASN n 1 53 THR n 1 54 SER n 1 55 ILE n 1 56 ILE n 1 57 GLN n 1 58 GLU n 1 59 SER n 1 60 CYS n 1 61 ASP n 1 62 LYS n 1 63 HIS n 1 64 TYR n 1 65 TRP n 1 66 ASP n 1 67 THR n 1 68 ILE n 1 69 ARG n 1 70 PHE n 1 71 ARG n 1 72 TYR n 1 73 CYS n 1 74 ALA n 1 75 PRO n 1 76 PRO n 1 77 GLY n 1 78 TYR n 1 79 ALA n 1 80 LEU n 1 81 LEU n 1 82 ARG n 1 83 CYS n 1 84 ASN n 1 85 ASP n 1 86 THR n 1 87 ASN n 1 88 TYR n 1 89 SER n 1 90 GLY n 1 91 PHE n 1 92 MET n 1 93 PRO n 1 94 LYS n 1 95 CYS n 1 96 SER n 1 97 LYS n 1 98 VAL n 1 99 VAL n 1 100 VAL n 1 101 SER n 1 102 SER n 1 103 CYS n 1 104 THR n 1 105 ARG n 1 106 MET n 1 107 MET n 1 108 GLU n 1 109 THR n 1 110 GLN n 1 111 THR n 1 112 SER n 1 113 THR n 1 114 TRP n 1 115 PHE n 1 116 GLY n 1 117 PHE n 1 118 ASN n 1 119 GLY n 1 120 THR n 1 121 ARG n 1 122 ALA n 1 123 GLU n 1 124 ASN n 1 125 ARG n 1 126 THR n 1 127 TYR n 1 128 ILE n 1 129 TYR n 1 130 TRP n 1 131 HIS n 1 132 GLY n 1 133 ARG n 1 134 ASP n 1 135 ASN n 1 136 ARG n 1 137 THR n 1 138 ILE n 1 139 ILE n 1 140 SER n 1 141 LEU n 1 142 ASN n 1 143 LYS n 1 144 TYR n 1 145 TYR n 1 146 ASN n 1 147 LEU n 1 148 THR n 1 149 MET n 1 150 LYS n 1 151 CYS n 1 152 ARG n 1 153 GLY n 1 154 ALA n 1 155 GLY n 1 156 TRP n 1 157 CYS n 1 158 TRP n 1 159 PHE n 1 160 GLY n 1 161 GLY n 1 162 ASN n 1 163 TRP n 1 164 LYS n 1 165 ASP n 1 166 ALA n 1 167 ILE n 1 168 LYS n 1 169 GLU n 1 170 MET n 1 171 LYS n 1 172 GLN n 1 173 THR n 1 174 ILE n 1 175 VAL n 1 176 LYS n 1 177 HIS n 1 178 PRO n 1 179 ARG n 1 180 TYR n 1 181 THR n 1 182 GLY n 1 183 THR n 1 184 ASN n 1 185 ASN n 1 186 THR n 1 187 ASP n 1 188 LYS n 1 189 ILE n 1 190 ASN n 1 191 LEU n 1 192 THR n 1 193 ALA n 1 194 PRO n 1 195 ARG n 1 196 GLY n 1 197 GLY n 1 198 ASP n 1 199 PRO n 1 200 GLU n 1 201 VAL n 1 202 THR n 1 203 PHE n 1 204 MET n 1 205 TRP n 1 206 THR n 1 207 ASN n 1 208 CYS n 1 209 ARG n 1 210 GLY n 1 211 GLU n 1 212 PHE n 1 213 LEU n 1 214 TYR n 1 215 CYS n 1 216 LYS n 1 217 MET n 1 218 ASN n 1 219 TRP n 1 220 PHE n 1 221 LEU n 1 222 ASN n 1 223 TRP n 1 224 VAL n 1 225 GLU n 1 226 ASP n 1 227 ARG n 1 228 ASP n 1 229 VAL n 1 230 THR n 1 231 ASN n 1 232 GLN n 1 233 ARG n 1 234 PRO n 1 235 LYS n 1 236 GLU n 1 237 ARG n 1 238 HIS n 1 239 ARG n 1 240 ARG n 1 241 ASN n 1 242 TYR n 1 243 VAL n 1 244 PRO n 1 245 CYS n 1 246 HIS n 1 247 ILE n 1 248 ARG n 1 249 GLN n 1 250 ILE n 1 251 ILE n 1 252 ASN n 1 253 THR n 1 254 TRP n 1 255 HIS n 1 256 LYS n 1 257 VAL n 1 258 GLY n 1 259 LYS n 1 260 ASN n 1 261 VAL n 1 262 TYR n 1 263 LEU n 1 264 PRO n 1 265 PRO n 1 266 ARG n 1 267 GLU n 1 268 GLY n 1 269 ASP n 1 270 LEU n 1 271 THR n 1 272 CYS n 1 273 ASN n 1 274 SER n 1 275 THR n 1 276 VAL n 1 277 THR n 1 278 SER n 1 279 LEU n 1 280 ILE n 1 281 ALA n 1 282 ASN n 1 283 ILE n 1 284 ASP n 1 285 TRP n 1 286 THR n 1 287 ASP n 1 288 GLY n 1 289 ASN n 1 290 GLN n 1 291 THR n 1 292 ASN n 1 293 ILE n 1 294 THR n 1 295 MET n 1 296 SER n 1 297 ALA n 1 298 GLU n 1 299 VAL n 1 300 ALA n 1 301 GLU n 1 302 LEU n 1 303 TYR n 1 304 ARG n 1 305 LEU n 1 306 GLU n 1 307 LEU n 1 308 GLY n 1 309 ASP n 1 310 TYR n 1 311 LYS n 1 312 LEU n 1 313 VAL n 1 314 GLU n 1 315 ILE n 1 316 THR n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name SIV _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain MAC32H _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'SIMIAN IMMUNODEFICIENCY VIRUS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 11723 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'TRICHOPLUSIA NI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7111 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line 'High Five' _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector PFAST-BAC1 _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PSIVGP120CORE _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 2BF1 1 ? ? 2BF1 ? 2 UNP Q07374 1 ? ? Q07374 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2BF1 A 1 ? 2 ? 2BF1 64 ? 65 ? 64 65 2 2 2BF1 A 3 ? 46 ? Q07374 66 ? 109 ? 66 109 3 1 2BF1 A 47 ? 47 ? 2BF1 110 ? 110 ? 110 110 4 1 2BF1 A 48 ? 49 ? 2BF1 207 ? 208 ? 207 208 5 2 2BF1 A 50 ? 152 ? Q07374 209 ? 311 ? 209 311 6 1 2BF1 A 153 ? 154 ? 2BF1 312 ? 313 ? 312 313 7 1 2BF1 A 155 ? 155 ? 2BF1 341 ? 341 ? 341 341 8 2 2BF1 A 156 ? 316 ? Q07374 342 ? 502 ? 342 502 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 BMA 'D-saccharide, beta linking' . beta-D-mannopyranose ? 'C6 H12 O6' 180.156 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 FUC 'L-saccharide, alpha linking' . alpha-L-fucopyranose ? 'C6 H12 O5' 164.156 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MAN 'D-saccharide, alpha linking' . alpha-D-mannopyranose ? 'C6 H12 O6' 180.156 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2BF1 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.98 _exptl_crystal.density_percent_sol 68.8 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.00 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6000, 100 MM SODIUM CITRATE, PH 5.0 AND 8% PEG 400 AT 20 DEGREES C.' # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date 2002-10-07 _diffrn_detector.details 'RH-COATED SI MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATER' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.916 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'CHESS BEAMLINE F1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline F1 _diffrn_source.pdbx_wavelength 0.916 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2BF1 _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 26.000 _reflns.d_resolution_high 4.000 _reflns.number_obs 100402 _reflns.number_all ? _reflns.percent_possible_obs 98.0 _reflns.pdbx_Rmerge_I_obs 0.08000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 12.0000 _reflns.B_iso_Wilson_estimate 141.10 _reflns.pdbx_redundancy 4.500 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 4.00 _reflns_shell.d_res_low 4.09 _reflns_shell.percent_possible_all 94.3 _reflns_shell.Rmerge_I_obs 0.82000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.300 _reflns_shell.pdbx_redundancy 4.00 _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2BF1 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 5842 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 26.00 _refine.ls_d_res_high 4.00 _refine.ls_percent_reflns_obs 98.0 _refine.ls_R_factor_obs 0.385 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.385 _refine.ls_R_factor_R_free 0.388 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.600 _refine.ls_number_reflns_R_free 279 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.809 _refine.correlation_coeff_Fo_to_Fc_free 0.857 _refine.B_iso_mean 128.80 _refine.aniso_B[1][1] 0.01000 _refine.aniso_B[2][2] 0.01000 _refine.aniso_B[3][3] -0.03000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 3.00 _refine.pdbx_solvent_ion_probe_radii 3.00 _refine.pdbx_solvent_shrinkage_radii 2.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PLEASE NOTE THAT BECAUSE OF THE LOW RESOLUTION OF THE EXPERIMENTAL DATA USED TO DETERMINE THIS STRUCTURE, THE PRECISION OF THE MODEL, PARTICULARLY WITH RESPECT TO SIDE CHAIN POSITIONS, IS REDUCED. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MIRAS _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOODWITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 1.153 _refine.overall_SU_ML 1.697 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 269.262 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2471 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 615 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 3086 _refine_hist.d_res_high 4.00 _refine_hist.d_res_low 26.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.014 0.021 ? 3207 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.067 2.150 ? 4433 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 8.116 5.000 ? 302 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 45.267 23.600 ? 125 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 24.209 15.000 ? 426 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 18.610 15.000 ? 19 'X-RAY DIFFRACTION' ? r_chiral_restr 0.112 0.200 ? 604 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 2043 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.341 0.200 ? 1715 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.344 0.200 ? 2100 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.268 0.200 ? 112 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.368 0.200 ? 82 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.194 0.200 ? 6 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 4.00 _refine_ls_shell.d_res_low 4.37 _refine_ls_shell.number_reflns_R_work 1309 _refine_ls_shell.R_factor_R_work 0.4030 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.5330 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 67 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 2BF1 _struct.title 'Structure of an unliganded and fully-glycosylated SIV gp120 envelope glycoprotein' _struct.pdbx_descriptor 'EXTERIOR MEMBRANE GLYCOPROTEIN GP120' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2BF1 _struct_keywords.pdbx_keywords 'VIRUS PROTEIN' _struct_keywords.text 'VIRUS PROTEIN, SIV, GP120, ENVELOPE GLYCOPROTEIN, AIDS, COAT PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 2 ? G N N 5 ? H N N 2 ? I N N 6 ? J N N 7 ? K N N 3 ? L N N 8 ? M N N 9 ? N N N 9 ? # _struct_biol.id 1 _struct_biol.details ;ALTHOUGH THIS ENTRY DESCRIBES THE MONOMERIC STRUCTURE OFGP120, A THEORETICAL MODEL OF THE TRIMERIC FORM OF THEPROTEIN HAS BEEN GENERATED. THE DETAILS OF THE TRIMER ANDTHE MATRICES RELATING CHAIN A OF THIS ENTRY TO THECONSTITUENTS OF THE TRIMERIC STRUCTURE CAN BE FOUND INREMARK 400 BELOW. ; # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASN A 17 ? GLU A 32 ? ASN A 80 GLU A 95 1 ? 16 HELX_P HELX_P2 2 MET A 106 ? THR A 109 ? MET A 265 THR A 268 1 ? 4 HELX_P HELX_P3 3 ASN A 162 ? HIS A 177 ? ASN A 348 HIS A 363 1 ? 16 HELX_P HELX_P4 4 ASN A 218 ? LEU A 221 ? ASN A 404 LEU A 407 1 ? 4 HELX_P HELX_P5 5 VAL A 299 ? LEU A 307 ? VAL A 485 LEU A 493 1 ? 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 38 SG ? ? ? 1_555 A CYS 60 SG ? ? A CYS 101 A CYS 219 1_555 ? ? ? ? ? ? ? 2.019 ? ? disulf2 disulf ? ? A CYS 45 SG ? ? ? 1_555 A CYS 51 SG ? ? A CYS 108 A CYS 210 1_555 ? ? ? ? ? ? ? 2.027 ? ? disulf3 disulf ? ? A CYS 73 SG ? ? ? 1_555 A CYS 103 SG ? ? A CYS 232 A CYS 262 1_555 ? ? ? ? ? ? ? 2.042 ? ? disulf4 disulf ? ? A CYS 83 SG ? ? ? 1_555 A CYS 95 SG ? ? A CYS 242 A CYS 254 1_555 ? ? ? ? ? ? ? 2.022 ? ? disulf5 disulf ? ? A CYS 151 SG ? ? ? 1_555 A CYS 157 SG ? ? A CYS 310 A CYS 343 1_555 ? ? ? ? ? ? ? 2.050 ? ? disulf6 disulf ? ? A CYS 208 SG ? ? ? 1_555 A CYS 272 SG ? ? A CYS 394 A CYS 458 1_555 ? ? ? ? ? ? ? 2.036 ? ? disulf7 disulf ? ? A CYS 215 SG ? ? ? 1_555 A CYS 245 SG ? ? A CYS 401 A CYS 431 1_555 ? ? ? ? ? ? ? 2.042 ? ? covale1 covale one ? A ASN 7 ND2 ? ? ? 1_555 M NAG . C1 ? ? A ASN 70 A NAG 1500 1_555 ? ? ? ? ? ? ? 1.449 ? N-Glycosylation covale2 covale one ? A ASN 52 ND2 ? ? ? 1_555 N NAG . C1 ? ? A ASN 211 A NAG 1501 1_555 ? ? ? ? ? ? ? 1.461 ? N-Glycosylation covale3 covale one ? A ASN 84 ND2 ? ? ? 1_555 K NAG . C1 ? ? A ASN 243 K NAG 1 1_555 ? ? ? ? ? ? ? 1.460 ? N-Glycosylation covale4 covale one ? A ASN 87 ND2 ? ? ? 1_555 B NAG . C1 ? ? A ASN 246 B NAG 1 1_555 ? ? ? ? ? ? ? 1.440 ? N-Glycosylation covale5 covale one ? A ASN 118 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 277 C NAG 1 1_555 ? ? ? ? ? ? ? 1.434 ? N-Glycosylation covale6 covale one ? A ASN 124 ND2 ? ? ? 1_555 D NAG . C1 ? ? A ASN 283 D NAG 1 1_555 ? ? ? ? ? ? ? 1.447 ? N-Glycosylation covale7 covale one ? A ASN 135 ND2 ? ? ? 1_555 E NAG . C1 ? ? A ASN 294 E NAG 1 1_555 ? ? ? ? ? ? ? 1.458 ? N-Glycosylation covale8 covale one ? A ASN 146 ND2 ? ? ? 1_555 F NAG . C1 ? ? A ASN 305 F NAG 1 1_555 ? ? ? ? ? ? ? 1.448 ? N-Glycosylation covale9 covale one ? A ASN 184 ND2 ? ? ? 1_555 G NAG . C1 ? ? A ASN 370 G NAG 1 1_555 ? ? ? ? ? ? ? 1.449 ? N-Glycosylation covale10 covale one ? A ASN 190 ND2 ? ? ? 1_555 H NAG . C1 ? ? A ASN 376 H NAG 1 1_555 ? ? ? ? ? ? ? 1.462 ? N-Glycosylation covale11 covale one ? A ASN 273 ND2 ? ? ? 1_555 I NAG . C1 ? ? A ASN 459 I NAG 1 1_555 ? ? ? ? ? ? ? 1.464 ? N-Glycosylation covale12 covale one ? A ASN 289 ND2 ? ? ? 1_555 J NAG . C1 ? ? A ASN 475 J NAG 1 1_555 ? ? ? ? ? ? ? 1.458 ? N-Glycosylation covale13 covale one ? A ASN 292 ND2 ? ? ? 1_555 L NAG . C1 ? ? A ASN 478 L NAG 1 1_555 ? ? ? ? ? ? ? 1.431 ? N-Glycosylation covale14 covale both ? B NAG . O4 ? ? ? 1_555 B NAG . C1 ? ? B NAG 1 B NAG 2 1_555 ? ? ? ? ? ? ? 1.453 ? ? covale15 covale one ? B NAG . O6 ? ? ? 1_555 B FUC . C1 ? ? B NAG 1 B FUC 4 1_555 ? ? ? ? ? ? ? 1.418 ? ? covale16 covale both ? B NAG . O4 ? ? ? 1_555 B BMA . C1 ? ? B NAG 2 B BMA 3 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale17 covale both ? C NAG . O4 ? ? ? 1_555 C NAG . C1 ? ? C NAG 1 C NAG 2 1_555 ? ? ? ? ? ? ? 1.458 ? ? covale18 covale one ? C NAG . O6 ? ? ? 1_555 C FUC . C1 ? ? C NAG 1 C FUC 6 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale19 covale both ? C NAG . O4 ? ? ? 1_555 C BMA . C1 ? ? C NAG 2 C BMA 3 1_555 ? ? ? ? ? ? ? 1.458 ? ? covale20 covale one ? C BMA . O3 ? ? ? 1_555 C MAN . C1 ? ? C BMA 3 C MAN 4 1_555 ? ? ? ? ? ? ? 1.454 ? ? covale21 covale one ? C BMA . O6 ? ? ? 1_555 C MAN . C1 ? ? C BMA 3 C MAN 5 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale22 covale both ? D NAG . O4 ? ? ? 1_555 D NAG . C1 ? ? D NAG 1 D NAG 2 1_555 ? ? ? ? ? ? ? 1.461 ? ? covale23 covale one ? D NAG . O6 ? ? ? 1_555 D FUC . C1 ? ? D NAG 1 D FUC 3 1_555 ? ? ? ? ? ? ? 1.443 ? ? covale24 covale both ? E NAG . O4 ? ? ? 1_555 E NAG . C1 ? ? E NAG 1 E NAG 2 1_555 ? ? ? ? ? ? ? 1.452 ? ? covale25 covale one ? E NAG . O6 ? ? ? 1_555 E FUC . C1 ? ? E NAG 1 E FUC 3 1_555 ? ? ? ? ? ? ? 1.455 ? ? covale26 covale both ? F NAG . O4 ? ? ? 1_555 F NAG . C1 ? ? F NAG 1 F NAG 2 1_555 ? ? ? ? ? ? ? 1.431 ? ? covale27 covale one ? F NAG . O6 ? ? ? 1_555 F FUC . C1 ? ? F NAG 1 F FUC 4 1_555 ? ? ? ? ? ? ? 1.438 ? ? covale28 covale both ? F NAG . O4 ? ? ? 1_555 F BMA . C1 ? ? F NAG 2 F BMA 3 1_555 ? ? ? ? ? ? ? 1.452 ? ? covale29 covale both ? G NAG . O4 ? ? ? 1_555 G NAG . C1 ? ? G NAG 1 G NAG 2 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale30 covale both ? H NAG . O4 ? ? ? 1_555 H NAG . C1 ? ? H NAG 1 H NAG 2 1_555 ? ? ? ? ? ? ? 1.446 ? ? covale31 covale one ? H NAG . O6 ? ? ? 1_555 H FUC . C1 ? ? H NAG 1 H FUC 4 1_555 ? ? ? ? ? ? ? 1.442 ? ? covale32 covale both ? H NAG . O4 ? ? ? 1_555 H BMA . C1 ? ? H NAG 2 H BMA 3 1_555 ? ? ? ? ? ? ? 1.466 ? ? covale33 covale both ? I NAG . O4 ? ? ? 1_555 I NAG . C1 ? ? I NAG 1 I NAG 2 1_555 ? ? ? ? ? ? ? 1.451 ? ? covale34 covale both ? I NAG . O4 ? ? ? 1_555 I BMA . C1 ? ? I NAG 2 I BMA 3 1_555 ? ? ? ? ? ? ? 1.446 ? ? covale35 covale one ? I BMA . O3 ? ? ? 1_555 I MAN . C1 ? ? I BMA 3 I MAN 4 1_555 ? ? ? ? ? ? ? 1.459 ? ? covale36 covale one ? I BMA . O6 ? ? ? 1_555 I MAN . C1 ? ? I BMA 3 I MAN 7 1_555 ? ? ? ? ? ? ? 1.446 ? ? covale37 covale one ? I MAN . O2 ? ? ? 1_555 I MAN . C1 ? ? I MAN 4 I MAN 5 1_555 ? ? ? ? ? ? ? 1.537 ? ? covale38 covale one ? I MAN . O2 ? ? ? 1_555 I MAN . C1 ? ? I MAN 5 I MAN 6 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale39 covale both ? J NAG . O4 ? ? ? 1_555 J NAG . C1 ? ? J NAG 1 J NAG 2 1_555 ? ? ? ? ? ? ? 1.460 ? ? covale40 covale both ? J NAG . O4 ? ? ? 1_555 J BMA . C1 ? ? J NAG 2 J BMA 3 1_555 ? ? ? ? ? ? ? 1.467 ? ? covale41 covale one ? J BMA . O3 ? ? ? 1_555 J MAN . C1 ? ? J BMA 3 J MAN 4 1_555 ? ? ? ? ? ? ? 1.460 ? ? covale42 covale one ? J BMA . O6 ? ? ? 1_555 J MAN . C1 ? ? J BMA 3 J MAN 5 1_555 ? ? ? ? ? ? ? 1.444 ? ? covale43 covale both ? K NAG . O4 ? ? ? 1_555 K NAG . C1 ? ? K NAG 1 K NAG 2 1_555 ? ? ? ? ? ? ? 1.451 ? ? covale44 covale one ? K NAG . O6 ? ? ? 1_555 K FUC . C1 ? ? K NAG 1 K FUC 6 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale45 covale both ? K NAG . O4 ? ? ? 1_555 K BMA . C1 ? ? K NAG 2 K BMA 3 1_555 ? ? ? ? ? ? ? 1.450 ? ? covale46 covale one ? K BMA . O3 ? ? ? 1_555 K MAN . C1 ? ? K BMA 3 K MAN 4 1_555 ? ? ? ? ? ? ? 1.456 ? ? covale47 covale one ? K BMA . O6 ? ? ? 1_555 K MAN . C1 ? ? K BMA 3 K MAN 5 1_555 ? ? ? ? ? ? ? 1.451 ? ? covale48 covale both ? L NAG . O4 ? ? ? 1_555 L NAG . C1 ? ? L NAG 1 L NAG 2 1_555 ? ? ? ? ? ? ? 1.457 ? ? covale49 covale both ? L NAG . O4 ? ? ? 1_555 L BMA . C1 ? ? L NAG 2 L BMA 3 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale50 covale one ? L BMA . O6 ? ? ? 1_555 L MAN . C1 ? ? L BMA 3 L MAN 4 1_555 ? ? ? ? ? ? ? 1.454 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 3 ? AC ? 7 ? AD ? 6 ? AE ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel AC 1 2 ? anti-parallel AC 2 3 ? anti-parallel AC 3 4 ? anti-parallel AC 4 5 ? anti-parallel AC 5 6 ? anti-parallel AC 6 7 ? anti-parallel AD 1 2 ? anti-parallel AD 2 3 ? anti-parallel AD 3 4 ? anti-parallel AD 4 5 ? parallel AD 5 6 ? anti-parallel AE 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 VAL A 39 ? LEU A 44 ? VAL A 102 LEU A 107 AA 2 ASN A 52 ? GLN A 57 ? ASN A 211 GLN A 216 AB 1 LYS A 97 ? SER A 102 ? LYS A 256 SER A 261 AB 2 ALA A 79 ? CYS A 83 ? ALA A 238 CYS A 242 AB 3 LYS A 311 ? VAL A 313 ? LYS A 497 VAL A 499 AC 1 GLN A 110 ? THR A 113 ? GLN A 269 THR A 272 AC 2 THR A 202 ? CYS A 208 ? THR A 388 CYS A 394 AC 3 PHE A 212 ? LYS A 216 ? PHE A 398 LYS A 402 AC 4 TYR A 242 ? ILE A 247 ? TYR A 428 ILE A 433 AC 5 GLY A 155 ? GLY A 161 ? GLY A 341 GLY A 347 AC 6 ASN A 146 ? ARG A 152 ? ASN A 305 ARG A 311 AC 7 THR A 271 ? VAL A 276 ? THR A 457 VAL A 462 AD 1 THR A 126 ? TRP A 130 ? THR A 285 TRP A 289 AD 2 ILE A 138 ? LYS A 143 ? ILE A 297 LYS A 302 AD 3 THR A 277 ? TRP A 285 ? THR A 463 TRP A 471 AD 4 GLN A 290 ? MET A 295 ? GLN A 476 MET A 481 AD 5 ASP A 187 ? ASN A 190 ? ASP A 373 ASN A 376 AD 6 VAL A 224 ? ARG A 227 ? VAL A 410 ARG A 413 AE 1 ILE A 250 ? TRP A 254 ? ILE A 436 TRP A 440 AE 2 GLY A 258 ? TYR A 262 ? GLY A 444 TYR A 448 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N LYS A 40 ? N LYS A 103 O ILE A 56 ? O ILE A 215 AB 1 2 O SER A 101 ? O SER A 260 N LEU A 80 ? N LEU A 239 AB 2 3 N LEU A 81 ? N LEU A 240 O LYS A 311 ? O LYS A 497 AC 1 2 N THR A 111 ? N THR A 270 O ASN A 207 ? O ASN A 393 AC 2 3 N THR A 206 ? N THR A 392 O LEU A 213 ? O LEU A 399 AC 3 4 O TYR A 214 ? O TYR A 400 N HIS A 246 ? N HIS A 432 AC 4 5 N CYS A 245 ? N CYS A 431 O GLY A 155 ? O GLY A 341 AC 5 6 O GLY A 160 ? O GLY A 346 N THR A 148 ? N THR A 307 AC 6 7 O CYS A 151 ? O CYS A 310 N CYS A 272 ? N CYS A 458 AD 1 2 N TYR A 127 ? N TYR A 286 O ASN A 142 ? O ASN A 301 AD 2 3 N ILE A 139 ? N ILE A 298 O ALA A 281 ? O ALA A 467 AD 3 4 N ASP A 284 ? N ASP A 470 O ASN A 292 ? O ASN A 478 AD 4 5 N ILE A 293 ? N ILE A 479 O ASN A 190 ? O ASN A 376 AD 5 6 O ILE A 189 ? O ILE A 375 N GLU A 225 ? N GLU A 411 AE 1 2 N ILE A 251 ? N ILE A 437 O ASN A 260 ? O ASN A 446 # _database_PDB_matrix.entry_id 2BF1 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2BF1 _atom_sites.fract_transf_matrix[1][1] 0.009255 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.009255 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.008496 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_ _database_PDB_caveat.id _database_PDB_caveat.text 1 'NAG B 1 HAS WRONG CHIRALITY AT ATOM C1' 2 'FUC B 4 HAS WRONG CHIRALITY AT ATOM C1' 3 'FUC C 6 HAS WRONG CHIRALITY AT ATOM C1' 4 'NAG D 1 HAS WRONG CHIRALITY AT ATOM C1' 5 'FUC D 3 HAS WRONG CHIRALITY AT ATOM C1' 6 'NAG E 1 HAS WRONG CHIRALITY AT ATOM C1' 7 'FUC E 3 HAS WRONG CHIRALITY AT ATOM C1' 8 'FUC F 4 HAS WRONG CHIRALITY AT ATOM C1' 9 'NAG G 1 HAS WRONG CHIRALITY AT ATOM C1' 10 'NAG H 1 HAS WRONG CHIRALITY AT ATOM C1' 11 'FUC H 4 HAS WRONG CHIRALITY AT ATOM C1' 12 'NAG I 1 HAS WRONG CHIRALITY AT ATOM C1' 13 'NAG K 1 HAS WRONG CHIRALITY AT ATOM C1' 14 'FUC K 6 HAS WRONG CHIRALITY AT ATOM C1' 15 'NAG L 1 HAS WRONG CHIRALITY AT ATOM C1' # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 HIS 1 64 64 HIS HIS A . n A 1 2 MET 2 65 65 MET MET A . n A 1 3 GLU 3 66 66 GLU GLU A . n A 1 4 LEU 4 67 67 LEU LEU A . n A 1 5 ALA 5 68 68 ALA ALA A . n A 1 6 LEU 6 69 69 LEU LEU A . n A 1 7 ASN 7 70 70 ASN ASN A . n A 1 8 VAL 8 71 71 VAL VAL A . n A 1 9 THR 9 72 72 THR THR A . n A 1 10 GLU 10 73 73 GLU GLU A . n A 1 11 SER 11 74 74 SER SER A . n A 1 12 PHE 12 75 75 PHE PHE A . n A 1 13 ASP 13 76 76 ASP ASP A . n A 1 14 ALA 14 77 77 ALA ALA A . n A 1 15 TRP 15 78 78 TRP TRP A . n A 1 16 GLU 16 79 79 GLU GLU A . n A 1 17 ASN 17 80 80 ASN ASN A . n A 1 18 THR 18 81 81 THR THR A . n A 1 19 VAL 19 82 82 VAL VAL A . n A 1 20 THR 20 83 83 THR THR A . n A 1 21 GLU 21 84 84 GLU GLU A . n A 1 22 GLN 22 85 85 GLN GLN A . n A 1 23 ALA 23 86 86 ALA ALA A . n A 1 24 ILE 24 87 87 ILE ILE A . n A 1 25 GLU 25 88 88 GLU GLU A . n A 1 26 ASP 26 89 89 ASP ASP A . n A 1 27 VAL 27 90 90 VAL VAL A . n A 1 28 TRP 28 91 91 TRP TRP A . n A 1 29 GLN 29 92 92 GLN GLN A . n A 1 30 LEU 30 93 93 LEU LEU A . n A 1 31 PHE 31 94 94 PHE PHE A . n A 1 32 GLU 32 95 95 GLU GLU A . n A 1 33 THR 33 96 96 THR THR A . n A 1 34 SER 34 97 97 SER SER A . n A 1 35 ILE 35 98 98 ILE ILE A . n A 1 36 LYS 36 99 99 LYS LYS A . n A 1 37 PRO 37 100 100 PRO PRO A . n A 1 38 CYS 38 101 101 CYS CYS A . n A 1 39 VAL 39 102 102 VAL VAL A . n A 1 40 LYS 40 103 103 LYS LYS A . n A 1 41 LEU 41 104 104 LEU LEU A . n A 1 42 SER 42 105 105 SER SER A . n A 1 43 PRO 43 106 106 PRO PRO A . n A 1 44 LEU 44 107 107 LEU LEU A . n A 1 45 CYS 45 108 108 CYS CYS A . n A 1 46 ILE 46 109 109 ILE ILE A . n A 1 47 GLY 47 110 110 GLY GLY A . n A 1 48 ALA 48 207 207 ALA ALA A . n A 1 49 GLY 49 208 208 GLY GLY A . n A 1 50 HIS 50 209 209 HIS HIS A . n A 1 51 CYS 51 210 210 CYS CYS A . n A 1 52 ASN 52 211 211 ASN ASN A . n A 1 53 THR 53 212 212 THR THR A . n A 1 54 SER 54 213 213 SER SER A . n A 1 55 ILE 55 214 214 ILE ILE A . n A 1 56 ILE 56 215 215 ILE ILE A . n A 1 57 GLN 57 216 216 GLN GLN A . n A 1 58 GLU 58 217 217 GLU GLU A . n A 1 59 SER 59 218 218 SER SER A . n A 1 60 CYS 60 219 219 CYS CYS A . n A 1 61 ASP 61 220 ? ? ? A . n A 1 62 LYS 62 221 ? ? ? A . n A 1 63 HIS 63 222 ? ? ? A . n A 1 64 TYR 64 223 ? ? ? A . n A 1 65 TRP 65 224 ? ? ? A . n A 1 66 ASP 66 225 ? ? ? A . n A 1 67 THR 67 226 ? ? ? A . n A 1 68 ILE 68 227 ? ? ? A . n A 1 69 ARG 69 228 ? ? ? A . n A 1 70 PHE 70 229 229 PHE PHE A . n A 1 71 ARG 71 230 230 ARG ARG A . n A 1 72 TYR 72 231 231 TYR TYR A . n A 1 73 CYS 73 232 232 CYS CYS A . n A 1 74 ALA 74 233 233 ALA ALA A . n A 1 75 PRO 75 234 234 PRO PRO A . n A 1 76 PRO 76 235 235 PRO PRO A . n A 1 77 GLY 77 236 236 GLY GLY A . n A 1 78 TYR 78 237 237 TYR TYR A . n A 1 79 ALA 79 238 238 ALA ALA A . n A 1 80 LEU 80 239 239 LEU LEU A . n A 1 81 LEU 81 240 240 LEU LEU A . n A 1 82 ARG 82 241 241 ARG ARG A . n A 1 83 CYS 83 242 242 CYS CYS A . n A 1 84 ASN 84 243 243 ASN ASN A . n A 1 85 ASP 85 244 244 ASP ASP A . n A 1 86 THR 86 245 245 THR THR A . n A 1 87 ASN 87 246 246 ASN ASN A . n A 1 88 TYR 88 247 247 TYR TYR A . n A 1 89 SER 89 248 248 SER SER A . n A 1 90 GLY 90 249 249 GLY GLY A . n A 1 91 PHE 91 250 250 PHE PHE A . n A 1 92 MET 92 251 251 MET MET A . n A 1 93 PRO 93 252 252 PRO PRO A . n A 1 94 LYS 94 253 253 LYS LYS A . n A 1 95 CYS 95 254 254 CYS CYS A . n A 1 96 SER 96 255 255 SER SER A . n A 1 97 LYS 97 256 256 LYS LYS A . n A 1 98 VAL 98 257 257 VAL VAL A . n A 1 99 VAL 99 258 258 VAL VAL A . n A 1 100 VAL 100 259 259 VAL VAL A . n A 1 101 SER 101 260 260 SER SER A . n A 1 102 SER 102 261 261 SER SER A . n A 1 103 CYS 103 262 262 CYS CYS A . n A 1 104 THR 104 263 263 THR THR A . n A 1 105 ARG 105 264 264 ARG ARG A . n A 1 106 MET 106 265 265 MET MET A . n A 1 107 MET 107 266 266 MET MET A . n A 1 108 GLU 108 267 267 GLU GLU A . n A 1 109 THR 109 268 268 THR THR A . n A 1 110 GLN 110 269 269 GLN GLN A . n A 1 111 THR 111 270 270 THR THR A . n A 1 112 SER 112 271 271 SER SER A . n A 1 113 THR 113 272 272 THR THR A . n A 1 114 TRP 114 273 273 TRP TRP A . n A 1 115 PHE 115 274 274 PHE PHE A . n A 1 116 GLY 116 275 275 GLY GLY A . n A 1 117 PHE 117 276 276 PHE PHE A . n A 1 118 ASN 118 277 277 ASN ASN A . n A 1 119 GLY 119 278 278 GLY GLY A . n A 1 120 THR 120 279 279 THR THR A . n A 1 121 ARG 121 280 280 ARG ARG A . n A 1 122 ALA 122 281 281 ALA ALA A . n A 1 123 GLU 123 282 282 GLU GLU A . n A 1 124 ASN 124 283 283 ASN ASN A . n A 1 125 ARG 125 284 284 ARG ARG A . n A 1 126 THR 126 285 285 THR THR A . n A 1 127 TYR 127 286 286 TYR TYR A . n A 1 128 ILE 128 287 287 ILE ILE A . n A 1 129 TYR 129 288 288 TYR TYR A . n A 1 130 TRP 130 289 289 TRP TRP A . n A 1 131 HIS 131 290 290 HIS HIS A . n A 1 132 GLY 132 291 291 GLY GLY A . n A 1 133 ARG 133 292 292 ARG ARG A . n A 1 134 ASP 134 293 293 ASP ASP A . n A 1 135 ASN 135 294 294 ASN ASN A . n A 1 136 ARG 136 295 295 ARG ARG A . n A 1 137 THR 137 296 296 THR THR A . n A 1 138 ILE 138 297 297 ILE ILE A . n A 1 139 ILE 139 298 298 ILE ILE A . n A 1 140 SER 140 299 299 SER SER A . n A 1 141 LEU 141 300 300 LEU LEU A . n A 1 142 ASN 142 301 301 ASN ASN A . n A 1 143 LYS 143 302 302 LYS LYS A . n A 1 144 TYR 144 303 303 TYR TYR A . n A 1 145 TYR 145 304 304 TYR TYR A . n A 1 146 ASN 146 305 305 ASN ASN A . n A 1 147 LEU 147 306 306 LEU LEU A . n A 1 148 THR 148 307 307 THR THR A . n A 1 149 MET 149 308 308 MET MET A . n A 1 150 LYS 150 309 309 LYS LYS A . n A 1 151 CYS 151 310 310 CYS CYS A . n A 1 152 ARG 152 311 311 ARG ARG A . n A 1 153 GLY 153 312 312 GLY GLY A . n A 1 154 ALA 154 313 313 ALA ALA A . n A 1 155 GLY 155 341 341 GLY GLY A . n A 1 156 TRP 156 342 342 TRP TRP A . n A 1 157 CYS 157 343 343 CYS CYS A . n A 1 158 TRP 158 344 344 TRP TRP A . n A 1 159 PHE 159 345 345 PHE PHE A . n A 1 160 GLY 160 346 346 GLY GLY A . n A 1 161 GLY 161 347 347 GLY GLY A . n A 1 162 ASN 162 348 348 ASN ASN A . n A 1 163 TRP 163 349 349 TRP TRP A . n A 1 164 LYS 164 350 350 LYS LYS A . n A 1 165 ASP 165 351 351 ASP ASP A . n A 1 166 ALA 166 352 352 ALA ALA A . n A 1 167 ILE 167 353 353 ILE ILE A . n A 1 168 LYS 168 354 354 LYS LYS A . n A 1 169 GLU 169 355 355 GLU GLU A . n A 1 170 MET 170 356 356 MET MET A . n A 1 171 LYS 171 357 357 LYS LYS A . n A 1 172 GLN 172 358 358 GLN GLN A . n A 1 173 THR 173 359 359 THR THR A . n A 1 174 ILE 174 360 360 ILE ILE A . n A 1 175 VAL 175 361 361 VAL VAL A . n A 1 176 LYS 176 362 362 LYS LYS A . n A 1 177 HIS 177 363 363 HIS HIS A . n A 1 178 PRO 178 364 364 PRO PRO A . n A 1 179 ARG 179 365 365 ARG ARG A . n A 1 180 TYR 180 366 366 TYR TYR A . n A 1 181 THR 181 367 367 THR THR A . n A 1 182 GLY 182 368 368 GLY GLY A . n A 1 183 THR 183 369 369 THR THR A . n A 1 184 ASN 184 370 370 ASN ASN A . n A 1 185 ASN 185 371 371 ASN ASN A . n A 1 186 THR 186 372 372 THR THR A . n A 1 187 ASP 187 373 373 ASP ASP A . n A 1 188 LYS 188 374 374 LYS LYS A . n A 1 189 ILE 189 375 375 ILE ILE A . n A 1 190 ASN 190 376 376 ASN ASN A . n A 1 191 LEU 191 377 377 LEU LEU A . n A 1 192 THR 192 378 378 THR THR A . n A 1 193 ALA 193 379 379 ALA ALA A . n A 1 194 PRO 194 380 380 PRO PRO A . n A 1 195 ARG 195 381 381 ARG ARG A . n A 1 196 GLY 196 382 382 GLY GLY A . n A 1 197 GLY 197 383 383 GLY GLY A . n A 1 198 ASP 198 384 384 ASP ASP A . n A 1 199 PRO 199 385 385 PRO PRO A . n A 1 200 GLU 200 386 386 GLU GLU A . n A 1 201 VAL 201 387 387 VAL VAL A . n A 1 202 THR 202 388 388 THR THR A . n A 1 203 PHE 203 389 389 PHE PHE A . n A 1 204 MET 204 390 390 MET MET A . n A 1 205 TRP 205 391 391 TRP TRP A . n A 1 206 THR 206 392 392 THR THR A . n A 1 207 ASN 207 393 393 ASN ASN A . n A 1 208 CYS 208 394 394 CYS CYS A . n A 1 209 ARG 209 395 395 ARG ARG A . n A 1 210 GLY 210 396 396 GLY GLY A . n A 1 211 GLU 211 397 397 GLU GLU A . n A 1 212 PHE 212 398 398 PHE PHE A . n A 1 213 LEU 213 399 399 LEU LEU A . n A 1 214 TYR 214 400 400 TYR TYR A . n A 1 215 CYS 215 401 401 CYS CYS A . n A 1 216 LYS 216 402 402 LYS LYS A . n A 1 217 MET 217 403 403 MET MET A . n A 1 218 ASN 218 404 404 ASN ASN A . n A 1 219 TRP 219 405 405 TRP TRP A . n A 1 220 PHE 220 406 406 PHE PHE A . n A 1 221 LEU 221 407 407 LEU LEU A . n A 1 222 ASN 222 408 408 ASN ASN A . n A 1 223 TRP 223 409 409 TRP TRP A . n A 1 224 VAL 224 410 410 VAL VAL A . n A 1 225 GLU 225 411 411 GLU GLU A . n A 1 226 ASP 226 412 412 ASP ASP A . n A 1 227 ARG 227 413 413 ARG ARG A . n A 1 228 ASP 228 414 414 ASP ASP A . n A 1 229 VAL 229 415 415 VAL VAL A . n A 1 230 THR 230 416 416 THR THR A . n A 1 231 ASN 231 417 417 ASN ASN A . n A 1 232 GLN 232 418 418 GLN GLN A . n A 1 233 ARG 233 419 419 ARG ARG A . n A 1 234 PRO 234 420 420 PRO PRO A . n A 1 235 LYS 235 421 421 LYS LYS A . n A 1 236 GLU 236 422 422 GLU GLU A . n A 1 237 ARG 237 423 423 ARG ARG A . n A 1 238 HIS 238 424 424 HIS HIS A . n A 1 239 ARG 239 425 425 ARG ARG A . n A 1 240 ARG 240 426 426 ARG ARG A . n A 1 241 ASN 241 427 427 ASN ASN A . n A 1 242 TYR 242 428 428 TYR TYR A . n A 1 243 VAL 243 429 429 VAL VAL A . n A 1 244 PRO 244 430 430 PRO PRO A . n A 1 245 CYS 245 431 431 CYS CYS A . n A 1 246 HIS 246 432 432 HIS HIS A . n A 1 247 ILE 247 433 433 ILE ILE A . n A 1 248 ARG 248 434 434 ARG ARG A . n A 1 249 GLN 249 435 435 GLN GLN A . n A 1 250 ILE 250 436 436 ILE ILE A . n A 1 251 ILE 251 437 437 ILE ILE A . n A 1 252 ASN 252 438 438 ASN ASN A . n A 1 253 THR 253 439 439 THR THR A . n A 1 254 TRP 254 440 440 TRP TRP A . n A 1 255 HIS 255 441 441 HIS HIS A . n A 1 256 LYS 256 442 442 LYS LYS A . n A 1 257 VAL 257 443 443 VAL VAL A . n A 1 258 GLY 258 444 444 GLY GLY A . n A 1 259 LYS 259 445 445 LYS LYS A . n A 1 260 ASN 260 446 446 ASN ASN A . n A 1 261 VAL 261 447 447 VAL VAL A . n A 1 262 TYR 262 448 448 TYR TYR A . n A 1 263 LEU 263 449 449 LEU LEU A . n A 1 264 PRO 264 450 450 PRO PRO A . n A 1 265 PRO 265 451 451 PRO PRO A . n A 1 266 ARG 266 452 452 ARG ARG A . n A 1 267 GLU 267 453 453 GLU GLU A . n A 1 268 GLY 268 454 454 GLY GLY A . n A 1 269 ASP 269 455 455 ASP ASP A . n A 1 270 LEU 270 456 456 LEU LEU A . n A 1 271 THR 271 457 457 THR THR A . n A 1 272 CYS 272 458 458 CYS CYS A . n A 1 273 ASN 273 459 459 ASN ASN A . n A 1 274 SER 274 460 460 SER SER A . n A 1 275 THR 275 461 461 THR THR A . n A 1 276 VAL 276 462 462 VAL VAL A . n A 1 277 THR 277 463 463 THR THR A . n A 1 278 SER 278 464 464 SER SER A . n A 1 279 LEU 279 465 465 LEU LEU A . n A 1 280 ILE 280 466 466 ILE ILE A . n A 1 281 ALA 281 467 467 ALA ALA A . n A 1 282 ASN 282 468 468 ASN ASN A . n A 1 283 ILE 283 469 469 ILE ILE A . n A 1 284 ASP 284 470 470 ASP ASP A . n A 1 285 TRP 285 471 471 TRP TRP A . n A 1 286 THR 286 472 472 THR THR A . n A 1 287 ASP 287 473 473 ASP ASP A . n A 1 288 GLY 288 474 474 GLY GLY A . n A 1 289 ASN 289 475 475 ASN ASN A . n A 1 290 GLN 290 476 476 GLN GLN A . n A 1 291 THR 291 477 477 THR THR A . n A 1 292 ASN 292 478 478 ASN ASN A . n A 1 293 ILE 293 479 479 ILE ILE A . n A 1 294 THR 294 480 480 THR THR A . n A 1 295 MET 295 481 481 MET MET A . n A 1 296 SER 296 482 482 SER SER A . n A 1 297 ALA 297 483 483 ALA ALA A . n A 1 298 GLU 298 484 484 GLU GLU A . n A 1 299 VAL 299 485 485 VAL VAL A . n A 1 300 ALA 300 486 486 ALA ALA A . n A 1 301 GLU 301 487 487 GLU GLU A . n A 1 302 LEU 302 488 488 LEU LEU A . n A 1 303 TYR 303 489 489 TYR TYR A . n A 1 304 ARG 304 490 490 ARG ARG A . n A 1 305 LEU 305 491 491 LEU LEU A . n A 1 306 GLU 306 492 492 GLU GLU A . n A 1 307 LEU 307 493 493 LEU LEU A . n A 1 308 GLY 308 494 494 GLY GLY A . n A 1 309 ASP 309 495 495 ASP ASP A . n A 1 310 TYR 310 496 496 TYR TYR A . n A 1 311 LYS 311 497 497 LYS LYS A . n A 1 312 LEU 312 498 498 LEU LEU A . n A 1 313 VAL 313 499 499 VAL VAL A . n A 1 314 GLU 314 500 ? ? ? A . n A 1 315 ILE 315 501 ? ? ? A . n A 1 316 THR 316 502 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code M 9 NAG 1 1500 1500 NAG NAG A . N 9 NAG 1 1501 1501 NAG NAG A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 7 A ASN 70 ? ASN 'GLYCOSYLATION SITE' 2 A ASN 52 A ASN 211 ? ASN 'GLYCOSYLATION SITE' 3 A ASN 84 A ASN 243 ? ASN 'GLYCOSYLATION SITE' 4 A ASN 87 A ASN 246 ? ASN 'GLYCOSYLATION SITE' 5 A ASN 118 A ASN 277 ? ASN 'GLYCOSYLATION SITE' 6 A ASN 124 A ASN 283 ? ASN 'GLYCOSYLATION SITE' 7 A ASN 135 A ASN 294 ? ASN 'GLYCOSYLATION SITE' 8 A ASN 146 A ASN 305 ? ASN 'GLYCOSYLATION SITE' 9 A ASN 184 A ASN 370 ? ASN 'GLYCOSYLATION SITE' 10 A ASN 190 A ASN 376 ? ASN 'GLYCOSYLATION SITE' 11 A ASN 273 A ASN 459 ? ASN 'GLYCOSYLATION SITE' 12 A ASN 289 A ASN 475 ? ASN 'GLYCOSYLATION SITE' 13 A ASN 292 A ASN 478 ? ASN 'GLYCOSYLATION SITE' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-02-17 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2018-08-29 5 'Structure model' 2 1 2019-04-03 6 'Structure model' 2 2 2019-05-08 7 'Structure model' 3 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 7 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Atomic model' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Non-polymer description' 8 4 'Structure model' 'Structure summary' 9 5 'Structure model' 'Data collection' 10 5 'Structure model' 'Derived calculations' 11 5 'Structure model' 'Source and taxonomy' 12 6 'Structure model' 'Data collection' 13 6 'Structure model' 'Experimental preparation' 14 7 'Structure model' Advisory 15 7 'Structure model' 'Atomic model' 16 7 'Structure model' 'Data collection' 17 7 'Structure model' 'Derived calculations' 18 7 'Structure model' Other 19 7 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' database_PDB_caveat 4 4 'Structure model' entity 5 4 'Structure model' pdbx_entity_nonpoly 6 4 'Structure model' pdbx_nonpoly_scheme 7 4 'Structure model' pdbx_validate_chiral 8 4 'Structure model' struct_asym 9 4 'Structure model' struct_conn 10 4 'Structure model' struct_site_gen 11 5 'Structure model' entity_src_gen 12 5 'Structure model' struct_conn 13 6 'Structure model' exptl_crystal_grow 14 7 'Structure model' atom_site 15 7 'Structure model' chem_comp 16 7 'Structure model' database_PDB_caveat 17 7 'Structure model' entity 18 7 'Structure model' pdbx_branch_scheme 19 7 'Structure model' pdbx_chem_comp_identifier 20 7 'Structure model' pdbx_database_status 21 7 'Structure model' pdbx_entity_branch 22 7 'Structure model' pdbx_entity_branch_descriptor 23 7 'Structure model' pdbx_entity_branch_link 24 7 'Structure model' pdbx_entity_branch_list 25 7 'Structure model' pdbx_entity_nonpoly 26 7 'Structure model' pdbx_nonpoly_scheme 27 7 'Structure model' pdbx_struct_assembly_gen 28 7 'Structure model' pdbx_validate_chiral 29 7 'Structure model' pdbx_validate_close_contact 30 7 'Structure model' pdbx_validate_symm_contact 31 7 'Structure model' struct_asym 32 7 'Structure model' struct_conn 33 7 'Structure model' struct_site 34 7 'Structure model' struct_site_gen # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_chem_comp.formula' 2 4 'Structure model' '_chem_comp.formula_weight' 3 4 'Structure model' '_chem_comp.id' 4 4 'Structure model' '_chem_comp.mon_nstd_flag' 5 4 'Structure model' '_chem_comp.name' 6 4 'Structure model' '_chem_comp.type' 7 4 'Structure model' '_pdbx_nonpoly_scheme.entity_id' 8 4 'Structure model' '_pdbx_nonpoly_scheme.mon_id' 9 4 'Structure model' '_pdbx_nonpoly_scheme.pdb_mon_id' 10 4 'Structure model' '_struct_asym.entity_id' 11 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 4 'Structure model' '_struct_site_gen.auth_comp_id' 16 4 'Structure model' '_struct_site_gen.label_comp_id' 17 5 'Structure model' '_entity_src_gen.pdbx_host_org_cell_line' 18 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 19 6 'Structure model' '_exptl_crystal_grow.temp' 20 7 'Structure model' '_atom_site.B_iso_or_equiv' 21 7 'Structure model' '_atom_site.Cartn_x' 22 7 'Structure model' '_atom_site.Cartn_y' 23 7 'Structure model' '_atom_site.Cartn_z' 24 7 'Structure model' '_atom_site.auth_asym_id' 25 7 'Structure model' '_atom_site.auth_atom_id' 26 7 'Structure model' '_atom_site.auth_comp_id' 27 7 'Structure model' '_atom_site.auth_seq_id' 28 7 'Structure model' '_atom_site.label_asym_id' 29 7 'Structure model' '_atom_site.label_atom_id' 30 7 'Structure model' '_atom_site.label_comp_id' 31 7 'Structure model' '_atom_site.label_entity_id' 32 7 'Structure model' '_atom_site.type_symbol' 33 7 'Structure model' '_chem_comp.name' 34 7 'Structure model' '_chem_comp.type' 35 7 'Structure model' '_database_PDB_caveat.text' 36 7 'Structure model' '_pdbx_database_status.status_code_sf' 37 7 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 38 7 'Structure model' '_pdbx_validate_chiral.auth_asym_id' 39 7 'Structure model' '_pdbx_validate_chiral.auth_seq_id' 40 7 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_2' 41 7 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 42 7 'Structure model' '_pdbx_validate_symm_contact.auth_asym_id_1' 43 7 'Structure model' '_pdbx_validate_symm_contact.auth_asym_id_2' 44 7 'Structure model' '_pdbx_validate_symm_contact.auth_seq_id_1' 45 7 'Structure model' '_pdbx_validate_symm_contact.auth_seq_id_2' 46 7 'Structure model' '_struct_conn.pdbx_dist_value' 47 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 48 7 'Structure model' '_struct_conn.pdbx_role' 49 7 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 50 7 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 51 7 'Structure model' '_struct_conn.ptnr1_label_asym_id' 52 7 'Structure model' '_struct_conn.ptnr1_label_atom_id' 53 7 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 54 7 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 55 7 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 56 7 'Structure model' '_struct_conn.ptnr2_label_asym_id' 57 7 'Structure model' '_struct_conn.ptnr2_label_comp_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x -7.8277 _pdbx_refine_tls.origin_y 24.3101 _pdbx_refine_tls.origin_z 7.6839 _pdbx_refine_tls.T[1][1] 0.3099 _pdbx_refine_tls.T[2][2] 0.3770 _pdbx_refine_tls.T[3][3] -0.1065 _pdbx_refine_tls.T[1][2] 0.1841 _pdbx_refine_tls.T[1][3] 0.1642 _pdbx_refine_tls.T[2][3] -0.1204 _pdbx_refine_tls.L[1][1] 2.5980 _pdbx_refine_tls.L[2][2] 4.3451 _pdbx_refine_tls.L[3][3] 3.9816 _pdbx_refine_tls.L[1][2] 0.6658 _pdbx_refine_tls.L[1][3] -0.2382 _pdbx_refine_tls.L[2][3] 1.2659 _pdbx_refine_tls.S[1][1] 0.0795 _pdbx_refine_tls.S[1][2] 0.2841 _pdbx_refine_tls.S[1][3] 0.0143 _pdbx_refine_tls.S[2][1] -0.5748 _pdbx_refine_tls.S[2][2] -0.0061 _pdbx_refine_tls.S[2][3] 0.2420 _pdbx_refine_tls.S[3][1] 0.0411 _pdbx_refine_tls.S[3][2] -0.1310 _pdbx_refine_tls.S[3][3] -0.0735 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 64 ? ? A 499 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 A 1500 ? ? A 1549 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language DENZO 'data reduction' . ? 1 ? ? ? ? SCALEPACK 'data scaling' . ? 2 ? ? ? ? SOLVE phasing . ? 3 ? ? ? ? SHARP phasing . ? 4 ? ? ? ? REFMAC refinement 5.2.0003 ? 5 ? ? ? ? # _pdbx_entry_details.entry_id 2BF1 _pdbx_entry_details.compound_details ;GP120 IS PRODUCED FROM A PRECURSOR PROTEIN, GP160. THE PRECURSOR ASSEMBLES INTO A TRIMER, WHICH REMAINS INTACT AFTER CLEAVAGE OF GP160 TO GP120 AND GP41. A THEORETICAL MODEL OF THE POSITION AND ORIENTATION OF GP120 WITHIN THIS TRIMERIC ASSEMBLY HAS BEEN GENERATED. THE MODEL LACKS THE GP41 STRUCTURE, BUT SPACE HAS BEEN LEFT FOR GP41 AT THE BASE OF THE TRIMER, RESULTING IN GAPS BETWEEN THE GP120 CHAINS OF THE MODEL. THE TRIMER MODEL CAN BE GENERATED BY APPLYING THE FOLLOWING TRANSFORMATIONS TO THE COORDINATES OF CHAIN A OF THIS PDB ENTRY: TRANS1 1 -0.932060 0.211070 0.294480 1.43530 TRANS2 1 0.071796 -0.689070 0.721130 43.48100 TRANS3 1 0.355130 0.693270 0.627100 -12.91480 TRANS1 2 0.528220 -0.702280 0.477270 36.93710 TRANS2 2 0.771290 0.161790 -0.615570 -22.98340 TRANS3 2 0.355090 0.693270 0.627130 -12.91500 TRANS1 3 0.403860 0.491250 -0.771730 -38.37270 TRANS2 3 -0.843070 0.527350 -0.105510 -20.49850 TRANS3 3 0.355140 0.693230 0.627140 -12.91380 ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;IN THE EXPRESSION CONSTRUCT, SHORT LINKERS, GAG HAVE BEEN SUBSTITUTED FOR THE V1V2 AND V3 LOOPS. THAT IS, RESIDUES FROM 110 TO 208 WERE REPLACED BY 3 RESIDUES GAG. RESIDUES FROM 312 TO 341 WERE REPLACED BY THREE RESIDUES GAG. RESIDUES FROM 220 - 228 AND 500 - 502 ARE DISORDERED AND NOT SEEN IN THE ELECTRON DENSITY MAPS. ; _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A LYS 354 ? ? N A GLN 358 ? ? 1.91 2 1 N A ILE 437 ? ? O A ASN 446 ? ? 2.05 3 1 O A GLU 355 ? ? N A THR 359 ? ? 2.09 4 1 O A ASP 244 ? ? O6 K NAG 1 ? ? 2.13 5 1 O A TRP 91 ? ? OH A TYR 448 ? ? 2.18 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O3 B FUC 4 ? ? 1_555 O3 B FUC 4 ? ? 8_555 0.65 2 1 C3 B FUC 4 ? ? 1_555 O3 B FUC 4 ? ? 8_555 1.92 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A ASP 244 ? ? CG A ASP 244 ? ? OD2 A ASP 244 ? ? 123.77 118.30 5.47 0.90 N 2 1 CB A ASP 495 ? ? CG A ASP 495 ? ? OD2 A ASP 495 ? ? 123.80 118.30 5.50 0.90 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LEU A 67 ? ? -59.31 -156.83 2 1 LEU A 69 ? ? -151.59 83.55 3 1 SER A 74 ? ? -142.37 -142.78 4 1 ASN A 80 ? ? -46.76 150.36 5 1 THR A 81 ? ? -112.62 -93.21 6 1 THR A 83 ? ? -48.63 -80.46 7 1 SER A 97 ? ? -161.98 -11.10 8 1 PRO A 100 ? ? -105.26 -65.99 9 1 CYS A 101 ? ? -161.56 -50.69 10 1 PRO A 106 ? ? -86.18 -146.70 11 1 LEU A 107 ? ? 165.29 54.66 12 1 ILE A 109 ? ? -158.72 0.44 13 1 HIS A 209 ? ? -162.91 -163.98 14 1 GLU A 217 ? ? 174.39 -142.61 15 1 SER A 218 ? ? -97.76 -155.44 16 1 CYS A 232 ? ? -66.53 -79.12 17 1 ALA A 233 ? ? -174.44 -46.46 18 1 PRO A 235 ? ? -62.25 72.65 19 1 CYS A 242 ? ? -65.48 -112.95 20 1 ASN A 243 ? ? 161.40 164.06 21 1 ASP A 244 ? ? 141.76 -86.29 22 1 SER A 248 ? ? -153.72 -67.94 23 1 MET A 251 ? ? 77.19 75.41 24 1 SER A 255 ? ? -135.23 -93.99 25 1 SER A 261 ? ? -144.02 -64.20 26 1 CYS A 262 ? ? -41.61 154.82 27 1 THR A 263 ? ? -151.41 79.74 28 1 MET A 265 ? ? -18.50 -56.98 29 1 THR A 268 ? ? -76.04 -141.80 30 1 SER A 271 ? ? -172.16 148.71 31 1 TRP A 273 ? ? -109.09 -72.36 32 1 PHE A 276 ? ? -77.28 -99.24 33 1 THR A 279 ? ? 74.99 132.16 34 1 ARG A 280 ? ? 23.99 59.27 35 1 ASN A 283 ? ? -30.54 -70.43 36 1 THR A 285 ? ? -40.10 154.43 37 1 TYR A 288 ? ? -20.28 115.18 38 1 ARG A 292 ? ? -157.55 50.47 39 1 ASP A 293 ? ? 54.53 -43.95 40 1 ASN A 294 ? ? -140.59 -53.74 41 1 TYR A 304 ? ? -32.58 161.39 42 1 ASN A 348 ? ? -97.16 41.20 43 1 PRO A 364 ? ? -64.32 87.22 44 1 LYS A 374 ? ? -164.91 70.67 45 1 THR A 378 ? ? -156.59 -95.36 46 1 ALA A 379 ? ? 99.26 29.55 47 1 PRO A 380 ? ? -82.91 -117.98 48 1 ARG A 381 ? ? 138.16 104.88 49 1 PRO A 385 ? ? -93.41 -130.63 50 1 GLU A 386 ? ? 164.48 43.64 51 1 CYS A 394 ? ? -167.87 103.90 52 1 ARG A 395 ? ? 85.78 17.62 53 1 ARG A 413 ? ? -59.19 -78.32 54 1 THR A 439 ? ? 33.88 124.13 55 1 TRP A 440 ? ? -78.94 -79.41 56 1 HIS A 441 ? ? -49.39 -10.10 57 1 VAL A 443 ? ? -61.75 69.73 58 1 PRO A 451 ? ? -102.34 -165.16 59 1 ARG A 452 ? ? 179.17 150.67 60 1 GLU A 453 ? ? -118.07 52.45 61 1 CYS A 458 ? ? -27.49 157.34 62 1 SER A 460 ? ? -172.03 145.38 63 1 THR A 463 ? ? -154.83 -49.85 64 1 SER A 464 ? ? -101.69 79.03 65 1 ASP A 473 ? ? -39.27 119.40 66 1 ALA A 483 ? ? -173.79 76.20 67 1 GLU A 484 ? ? -79.62 -146.92 68 1 LEU A 493 ? ? -67.61 -96.09 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C1 ? B NAG 1 ? 'WRONG HAND' . 2 1 C1 ? B FUC 4 ? 'WRONG HAND' . 3 1 C1 ? C FUC 6 ? 'WRONG HAND' . 4 1 C1 ? D NAG 1 ? 'WRONG HAND' . 5 1 C1 ? D FUC 3 ? 'WRONG HAND' . 6 1 C1 ? E NAG 1 ? 'WRONG HAND' . 7 1 C1 ? E FUC 3 ? 'WRONG HAND' . 8 1 C1 ? F FUC 4 ? 'WRONG HAND' . 9 1 C1 ? G NAG 1 ? PLANAR . 10 1 C1 ? H NAG 1 ? PLANAR . 11 1 C1 ? H FUC 4 ? 'WRONG HAND' . 12 1 C1 ? I NAG 1 ? PLANAR . 13 1 C1 ? K NAG 1 ? PLANAR . 14 1 C1 ? K FUC 6 ? 'WRONG HAND' . 15 1 C1 ? L NAG 1 ? 'WRONG HAND' . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A ASP 220 ? A ASP 61 2 1 Y 1 A LYS 221 ? A LYS 62 3 1 Y 1 A HIS 222 ? A HIS 63 4 1 Y 1 A TYR 223 ? A TYR 64 5 1 Y 1 A TRP 224 ? A TRP 65 6 1 Y 1 A ASP 225 ? A ASP 66 7 1 Y 1 A THR 226 ? A THR 67 8 1 Y 1 A ILE 227 ? A ILE 68 9 1 Y 1 A ARG 228 ? A ARG 69 10 1 Y 1 A GLU 500 ? A GLU 314 11 1 Y 1 A ILE 501 ? A ILE 315 12 1 Y 1 A THR 502 ? A THR 316 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero B 2 NAG 1 B NAG 1 A NDG 1502 n B 2 NAG 2 B NAG 2 A NAG 1503 n B 2 BMA 3 B BMA 3 A BMA 1504 n B 2 FUC 4 B FUC 4 A FUC 1505 n C 3 NAG 1 C NAG 1 A NAG 1506 n C 3 NAG 2 C NAG 2 A NAG 1507 n C 3 BMA 3 C BMA 3 A BMA 1508 n C 3 MAN 4 C MAN 4 A MAN 1509 n C 3 MAN 5 C MAN 5 A MAN 1510 n C 3 FUC 6 C FUC 6 A FUC 1511 n D 4 NAG 1 D NAG 1 A NDG 1512 n D 4 NAG 2 D NAG 2 A NAG 1513 n D 4 FUC 3 D FUC 3 A FUC 1514 n E 4 NAG 1 E NAG 1 A NDG 1515 n E 4 NAG 2 E NAG 2 A NAG 1516 n E 4 FUC 3 E FUC 3 A FUC 1517 n F 2 NAG 1 F NAG 1 A NAG 1518 n F 2 NAG 2 F NAG 2 A NAG 1519 n F 2 BMA 3 F BMA 3 A BMA 1520 n F 2 FUC 4 F FUC 4 A FUC 1521 n G 5 NAG 1 G NAG 1 A NDG 1522 n G 5 NAG 2 G NAG 2 A NAG 1523 n H 2 NAG 1 H NAG 1 A NDG 1524 n H 2 NAG 2 H NAG 2 A NAG 1525 n H 2 BMA 3 H BMA 3 A BMA 1526 n H 2 FUC 4 H FUC 4 A FUC 1527 n I 6 NAG 1 I NAG 1 A NAG 1528 n I 6 NAG 2 I NAG 2 A NAG 1529 n I 6 BMA 3 I BMA 3 A BMA 1530 n I 6 MAN 4 I MAN 4 A MAN 1531 n I 6 MAN 5 I MAN 5 A MAN 1532 n I 6 MAN 6 I MAN 6 A MAN 1533 n I 6 MAN 7 I MAN 7 A MAN 1534 n J 7 NAG 1 J NAG 1 A NAG 1535 n J 7 NAG 2 J NAG 2 A NAG 1536 n J 7 BMA 3 J BMA 3 A BMA 1537 n J 7 MAN 4 J MAN 4 A MAN 1538 n J 7 MAN 5 J MAN 5 A MAN 1539 n K 3 NAG 1 K NAG 1 A NAG 1540 n K 3 NAG 2 K NAG 2 A NAG 1541 n K 3 BMA 3 K BMA 3 A BMA 1542 n K 3 MAN 4 K MAN 4 A MAN 1543 n K 3 MAN 5 K MAN 5 A MAN 1544 n K 3 FUC 6 K FUC 6 A FUC 1545 n L 8 NAG 1 L NAG 1 A NDG 1546 n L 8 NAG 2 L NAG 2 A NAG 1547 n L 8 BMA 3 L BMA 3 A BMA 1548 n L 8 MAN 4 L MAN 4 A MAN 1549 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BMA 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DManpb BMA 'COMMON NAME' GMML 1.0 b-D-mannopyranose BMA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Manp BMA 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Man FUC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 LFucpa FUC 'COMMON NAME' GMML 1.0 a-L-fucopyranose FUC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-L-Fucp FUC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Fuc MAN 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DManpa MAN 'COMMON NAME' GMML 1.0 a-D-mannopyranose MAN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Manp MAN 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Man NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide 7 oligosaccharide 8 oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 'DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 2 2 'WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1' WURCS PDB2Glycan 1.1.0 3 2 '[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}' LINUCS PDB-CARE ? 4 3 'DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 5 3 'WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1' WURCS PDB2Glycan 1.1.0 6 3 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}' LINUCS PDB-CARE ? 7 4 'DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 8 4 'WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1' WURCS PDB2Glycan 1.1.0 9 4 '[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}' LINUCS PDB-CARE ? 10 5 DGlcpNAcb1-4DGlcpNAcb1- 'Glycam Condensed Sequence' GMML 1.0 11 5 'WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1' WURCS PDB2Glycan 1.1.0 12 5 '[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}' LINUCS PDB-CARE ? 13 6 'DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 14 6 'WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1' WURCS PDB2Glycan 1.1.0 15 6 ;[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}}} ; LINUCS PDB-CARE ? 16 7 'DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 17 7 'WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1' WURCS PDB2Glycan 1.1.0 18 7 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}' LINUCS PDB-CARE ? 19 8 DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1- 'Glycam Condensed Sequence' GMML 1.0 20 8 'WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1' WURCS PDB2Glycan 1.1.0 21 8 '[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}' LINUCS PDB-CARE ? # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 2 2 NAG C1 O1 1 NAG O4 HO4 sing ? 2 2 3 BMA C1 O1 2 NAG O4 HO4 sing ? 3 2 4 FUC C1 O1 1 NAG O6 HO6 sing ? 4 3 2 NAG C1 O1 1 NAG O4 HO4 sing ? 5 3 3 BMA C1 O1 2 NAG O4 HO4 sing ? 6 3 4 MAN C1 O1 3 BMA O3 HO3 sing ? 7 3 5 MAN C1 O1 3 BMA O6 HO6 sing ? 8 3 6 FUC C1 O1 1 NAG O6 HO6 sing ? 9 4 2 NAG C1 O1 1 NAG O4 HO4 sing ? 10 4 3 FUC C1 O1 1 NAG O6 HO6 sing ? 11 5 2 NAG C1 O1 1 NAG O4 HO4 sing ? 12 6 2 NAG C1 O1 1 NAG O4 HO4 sing ? 13 6 3 BMA C1 O1 2 NAG O4 HO4 sing ? 14 6 4 MAN C1 O1 3 BMA O3 HO3 sing ? 15 6 5 MAN C1 O1 4 MAN O2 HO2 sing ? 16 6 6 MAN C1 O1 5 MAN O2 HO2 sing ? 17 6 7 MAN C1 O1 3 BMA O6 HO6 sing ? 18 7 2 NAG C1 O1 1 NAG O4 HO4 sing ? 19 7 3 BMA C1 O1 2 NAG O4 HO4 sing ? 20 7 4 MAN C1 O1 3 BMA O3 HO3 sing ? 21 7 5 MAN C1 O1 3 BMA O6 HO6 sing ? 22 8 2 NAG C1 O1 1 NAG O4 HO4 sing ? 23 8 3 BMA C1 O1 2 NAG O4 HO4 sing ? 24 8 4 MAN C1 O1 3 BMA O6 HO6 sing ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 NAG 1 n 2 NAG 2 n 2 BMA 3 n 2 FUC 4 n 3 NAG 1 n 3 NAG 2 n 3 BMA 3 n 3 MAN 4 n 3 MAN 5 n 3 FUC 6 n 4 NAG 1 n 4 NAG 2 n 4 FUC 3 n 5 NAG 1 n 5 NAG 2 n 6 NAG 1 n 6 NAG 2 n 6 BMA 3 n 6 MAN 4 n 6 MAN 5 n 6 MAN 6 n 6 MAN 7 n 7 NAG 1 n 7 NAG 2 n 7 BMA 3 n 7 MAN 4 n 7 MAN 5 n 8 NAG 1 n 8 NAG 2 n 8 BMA 3 n 8 MAN 4 n # _pdbx_entity_nonpoly.entity_id 9 _pdbx_entity_nonpoly.name 2-acetamido-2-deoxy-beta-D-glucopyranose _pdbx_entity_nonpoly.comp_id NAG #