data_1ZA4 # _entry.id 1ZA4 # _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 1ZA4 RCSB RCSB032489 WWPDB D_1000032489 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1Z78 _pdbx_database_related.details 'Crystal Structure of the Thrombospondin-1 N-terminal Domain' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ZA4 _pdbx_database_status.recvd_initial_deposition_date 2005-04-05 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Tan, K.' 1 'Wang, J.H.' 2 'Lawler, J.' 3 # _citation.id primary _citation.title 'The Structures of the Thrombospondin-1 N-terminal Domain and its Complex with a Synthetic Pentameric Heparin' _citation.journal_abbrev Structure _citation.journal_volume 14 _citation.page_first 33 _citation.page_last 42 _citation.year 2006 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16407063 _citation.pdbx_database_id_DOI 10.1016/j.str.2005.09.017 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tan, K.' 1 ? primary 'Duquette, M.' 2 ? primary 'Liu, J.H.' 3 ? primary 'Zhang, R.' 4 ? primary 'Joachimiak, A.' 5 ? primary 'Wang, J.H.' 6 ? primary 'Lawler, J.' 7 ? # _cell.entry_id 1ZA4 _cell.length_a 42.404 _cell.length_b 53.053 _cell.length_c 92.723 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1ZA4 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # 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 'Thrombospondin 1' 27649.893 1 ? ? 'N-terminal Domain' ? 2 non-polymer man '2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose' 339.298 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 5 ? ? ? ? 4 water nat water 18.015 78 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDANLIPPVPDDKFQDLVDAVRTEKGFLLLASL RQ(MSE)KKTRGTLLALERKDHSGQVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDRAQLYID CEK(MSE)ENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQNVRFVFGTTPEDILRNKGCSSSTSVLLTLDNNV VNGSSPAIRTNTGHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDANLIPPVPDDKFQDLVDAVRTEKGFLLLASL RQMKKTRGTLLALERKDHSGQVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDRAQLYIDCEKM ENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQNVRFVFGTTPEDILRNKGCSSSTSVLLTLDNNVVNGSSPAI RTNTGHHHHHH ; _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 ARG n 1 2 SER n 1 3 PRO n 1 4 TRP n 1 5 ASN n 1 6 ARG n 1 7 ILE n 1 8 PRO n 1 9 GLU n 1 10 SER n 1 11 GLY n 1 12 GLY n 1 13 ASP n 1 14 ASN n 1 15 SER n 1 16 VAL n 1 17 PHE n 1 18 ASP n 1 19 ILE n 1 20 PHE n 1 21 GLU n 1 22 LEU n 1 23 THR n 1 24 GLY n 1 25 ALA n 1 26 ALA n 1 27 ARG n 1 28 LYS n 1 29 GLY n 1 30 SER n 1 31 GLY n 1 32 ARG n 1 33 ARG n 1 34 LEU n 1 35 VAL n 1 36 LYS n 1 37 GLY n 1 38 PRO n 1 39 ASP n 1 40 PRO n 1 41 SER n 1 42 SER n 1 43 PRO n 1 44 ALA n 1 45 PHE n 1 46 ARG n 1 47 ILE n 1 48 GLU n 1 49 ASP n 1 50 ALA n 1 51 ASN n 1 52 LEU n 1 53 ILE n 1 54 PRO n 1 55 PRO n 1 56 VAL n 1 57 PRO n 1 58 ASP n 1 59 ASP n 1 60 LYS n 1 61 PHE n 1 62 GLN n 1 63 ASP n 1 64 LEU n 1 65 VAL n 1 66 ASP n 1 67 ALA n 1 68 VAL n 1 69 ARG n 1 70 THR n 1 71 GLU n 1 72 LYS n 1 73 GLY n 1 74 PHE n 1 75 LEU n 1 76 LEU n 1 77 LEU n 1 78 ALA n 1 79 SER n 1 80 LEU n 1 81 ARG n 1 82 GLN n 1 83 MSE n 1 84 LYS n 1 85 LYS n 1 86 THR n 1 87 ARG n 1 88 GLY n 1 89 THR n 1 90 LEU n 1 91 LEU n 1 92 ALA n 1 93 LEU n 1 94 GLU n 1 95 ARG n 1 96 LYS n 1 97 ASP n 1 98 HIS n 1 99 SER n 1 100 GLY n 1 101 GLN n 1 102 VAL n 1 103 PHE n 1 104 SER n 1 105 VAL n 1 106 VAL n 1 107 SER n 1 108 ASN n 1 109 GLY n 1 110 LYS n 1 111 ALA n 1 112 GLY n 1 113 THR n 1 114 LEU n 1 115 ASP n 1 116 LEU n 1 117 SER n 1 118 LEU n 1 119 THR n 1 120 VAL n 1 121 GLN n 1 122 GLY n 1 123 LYS n 1 124 GLN n 1 125 HIS n 1 126 VAL n 1 127 VAL n 1 128 SER n 1 129 VAL n 1 130 GLU n 1 131 GLU n 1 132 ALA n 1 133 LEU n 1 134 LEU n 1 135 ALA n 1 136 THR n 1 137 GLY n 1 138 GLN n 1 139 TRP n 1 140 LYS n 1 141 SER n 1 142 ILE n 1 143 THR n 1 144 LEU n 1 145 PHE n 1 146 VAL n 1 147 GLN n 1 148 GLU n 1 149 ASP n 1 150 ARG n 1 151 ALA n 1 152 GLN n 1 153 LEU n 1 154 TYR n 1 155 ILE n 1 156 ASP n 1 157 CYS n 1 158 GLU n 1 159 LYS n 1 160 MSE n 1 161 GLU n 1 162 ASN n 1 163 ALA n 1 164 GLU n 1 165 LEU n 1 166 ASP n 1 167 VAL n 1 168 PRO n 1 169 ILE n 1 170 GLN n 1 171 SER n 1 172 VAL n 1 173 PHE n 1 174 THR n 1 175 ARG n 1 176 ASP n 1 177 LEU n 1 178 ALA n 1 179 SER n 1 180 ILE n 1 181 ALA n 1 182 ARG n 1 183 LEU n 1 184 ARG n 1 185 ILE n 1 186 ALA n 1 187 LYS n 1 188 GLY n 1 189 GLY n 1 190 VAL n 1 191 ASN n 1 192 ASP n 1 193 ASN n 1 194 PHE n 1 195 GLN n 1 196 GLY n 1 197 VAL n 1 198 LEU n 1 199 GLN n 1 200 ASN n 1 201 VAL n 1 202 ARG n 1 203 PHE n 1 204 VAL n 1 205 PHE n 1 206 GLY n 1 207 THR n 1 208 THR n 1 209 PRO n 1 210 GLU n 1 211 ASP n 1 212 ILE n 1 213 LEU n 1 214 ARG n 1 215 ASN n 1 216 LYS n 1 217 GLY n 1 218 CYS n 1 219 SER n 1 220 SER n 1 221 SER n 1 222 THR n 1 223 SER n 1 224 VAL n 1 225 LEU n 1 226 LEU n 1 227 THR n 1 228 LEU n 1 229 ASP n 1 230 ASN n 1 231 ASN n 1 232 VAL n 1 233 VAL n 1 234 ASN n 1 235 GLY n 1 236 SER n 1 237 SER n 1 238 PRO n 1 239 ALA n 1 240 ILE n 1 241 ARG n 1 242 THR n 1 243 ASN n 1 244 THR n 1 245 GLY n 1 246 HIS n 1 247 HIS n 1 248 HIS n 1 249 HIS n 1 250 HIS n 1 251 HIS 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 human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene 'THBS1, TSP, TSP1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 'fruit flies' _entity_src_gen.pdbx_host_org_scientific_name Drosophila _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7215 _entity_src_gen.host_org_genus Drosophila _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 'Drosophila S2 cell' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _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 plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name 'pMT/BiP/v5-His A' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TSP1_HUMAN _struct_ref.pdbx_db_accession P07996 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;NRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDANLIPPVPDDKFQDLVDAVRTEKGFLLLASLRQMK KTRGTLLALERKDHSGQVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDRAQLYIDCEKMENAE LDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQNVRFVFGTTPEDILRNKGCS ; _struct_ref.pdbx_align_begin 19 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1ZA4 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 5 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 219 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P07996 _struct_ref_seq.db_align_beg 19 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 233 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 215 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1ZA4 MSE A 83 ? UNP P07996 MET 97 'modified residue' 79 1 1 1ZA4 MSE A 160 ? UNP P07996 MET 174 'modified residue' 156 2 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 SGN 'D-saccharide, alpha linking' n '2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose' ? 'C6 H13 N O11 S2' 339.298 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 1ZA4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.0 _exptl_crystal.density_percent_sol 37.3 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_details '30% PEG1500 AND 0.1 M NAAC , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2004-10-31 ? 2 CCD 'ADSC QUANTUM 315' 2004-10-31 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M Graphite MAD x-ray 2 1 M Graphite 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.97923 1.0 2 0.97928 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'APS BEAMLINE 19-ID' APS 19-ID ? '0.97923, 0.97928' 2 SYNCHROTRON 'APS BEAMLINE 19-ID' APS 19-ID ? 0.97923 # _reflns.entry_id 1ZA4 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.9 _reflns.d_resolution_low 50 _reflns.number_all ? _reflns.number_obs 30776 _reflns.percent_possible_obs 96.7 _reflns.pdbx_Rmerge_I_obs 0.068 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 27.1 _reflns.B_iso_Wilson_estimate 28.7 _reflns.pdbx_redundancy 4.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.90 _reflns_shell.d_res_low 1.97 _reflns_shell.percent_possible_all 78.2 _reflns_shell.Rmerge_I_obs 0.359 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.85 _reflns_shell.pdbx_redundancy 2.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 2479 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1ZA4 _refine.ls_d_res_high 1.9 _refine.ls_d_res_low 25.0 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 29639 _refine.ls_number_reflns_obs 24904 _refine.ls_number_reflns_R_free 2443 _refine.ls_percent_reflns_obs 78.2 _refine.ls_R_factor_all 0.271 _refine.ls_R_factor_obs 0.253 _refine.ls_R_factor_R_work 0.245 _refine.ls_R_factor_R_free 0.275 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean 34.2 _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1ZA4 _refine_analyze.Luzzati_coordinate_error_obs 0.31 _refine_analyze.Luzzati_sigma_a_obs 0.15 _refine_analyze.Luzzati_d_res_low_obs 3 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1585 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 45 _refine_hist.number_atoms_solvent 78 _refine_hist.number_atoms_total 1708 _refine_hist.d_res_high 1.9 _refine_hist.d_res_low 25.0 # 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 c_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.43 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 26.31 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.25 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.9 _refine_ls_shell.d_res_low 1.97 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.256 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.259 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 115 _refine_ls_shell.number_reflns_obs 881 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 1ZA4 _struct.title 'Crystal Structure of the Thrombospondin-1 N-terminal Domain in Complex with Arixtra' _struct.pdbx_descriptor 'Thrombospondin 1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1ZA4 _struct_keywords.pdbx_keywords 'CELL ADHESION' _struct_keywords.text 'TSP-1, NTSP-1, HBD, ARIXTRA, CELL ADHESION' # 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 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? # 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 ILE A 19 ? GLY A 24 ? ILE A 15 GLY A 20 1 ? 6 HELX_P HELX_P2 2 ASP A 49 ? ILE A 53 ? ASP A 45 ILE A 49 5 ? 5 HELX_P HELX_P3 3 PRO A 57 ? LYS A 72 ? PRO A 53 LYS A 68 1 ? 16 HELX_P HELX_P4 4 PRO A 168 ? VAL A 172 ? PRO A 164 VAL A 168 5 ? 5 HELX_P HELX_P5 5 ASP A 176 ? SER A 179 ? ASP A 172 SER A 175 5 ? 4 HELX_P HELX_P6 6 THR A 208 ? LYS A 216 ? THR A 204 LYS A 212 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 covale1 covale both ? A GLN 82 C ? ? ? 1_555 A MSE 83 N ? ? A GLN 78 A MSE 79 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale2 covale both ? A MSE 83 C ? ? ? 1_555 A LYS 84 N ? ? A MSE 79 A LYS 80 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale3 covale both ? A LYS 159 C ? ? ? 1_555 A MSE 160 N ? ? A LYS 155 A MSE 156 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale4 covale both ? A MSE 160 C ? ? ? 1_555 A GLU 161 N ? ? A MSE 156 A GLU 157 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 6 ? C ? 5 ? # 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel C 4 5 ? 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 A 1 VAL A 16 ? ASP A 18 ? VAL A 12 ASP A 14 A 2 GLY A 196 ? VAL A 204 ? GLY A 192 VAL A 200 A 3 ALA A 44 ? ILE A 47 ? ALA A 40 ILE A 43 A 4 ARG A 32 ? VAL A 35 ? ARG A 28 VAL A 31 B 1 VAL A 16 ? ASP A 18 ? VAL A 12 ASP A 14 B 2 GLY A 196 ? VAL A 204 ? GLY A 192 VAL A 200 B 3 GLY A 73 ? GLN A 82 ? GLY A 69 GLN A 78 B 4 LYS A 140 ? GLN A 147 ? LYS A 136 GLN A 143 B 5 ARG A 150 ? ILE A 155 ? ARG A 146 ILE A 151 B 6 GLU A 161 ? GLU A 164 ? GLU A 157 GLU A 160 C 1 LYS A 123 ? VAL A 129 ? LYS A 119 VAL A 125 C 2 THR A 113 ? VAL A 120 ? THR A 109 VAL A 116 C 3 GLN A 101 ? ASN A 108 ? GLN A 97 ASN A 104 C 4 ARG A 87 ? ARG A 95 ? ARG A 83 ARG A 91 C 5 ALA A 181 ? ILE A 185 ? ALA A 177 ILE A 181 # 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 A 1 2 N PHE A 17 ? N PHE A 13 O PHE A 203 ? O PHE A 199 A 2 3 O GLY A 196 ? O GLY A 192 N ILE A 47 ? N ILE A 43 A 3 4 O ARG A 46 ? O ARG A 42 N ARG A 33 ? N ARG A 29 B 1 2 N PHE A 17 ? N PHE A 13 O PHE A 203 ? O PHE A 199 B 2 3 O ARG A 202 ? O ARG A 198 N LEU A 77 ? N LEU A 73 B 3 4 N LEU A 76 ? N LEU A 72 O LEU A 144 ? O LEU A 140 B 4 5 N PHE A 145 ? N PHE A 141 O GLN A 152 ? O GLN A 148 B 5 6 N LEU A 153 ? N LEU A 149 O GLU A 161 ? O GLU A 157 C 1 2 O HIS A 125 ? O HIS A 121 N LEU A 118 ? N LEU A 114 C 2 3 O ASP A 115 ? O ASP A 111 N VAL A 106 ? N VAL A 102 C 3 4 O VAL A 105 ? O VAL A 101 N LEU A 90 ? N LEU A 86 C 4 5 N ALA A 92 ? N ALA A 88 O ARG A 184 ? O ARG A 180 # _database_PDB_matrix.entry_id 1ZA4 _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 1ZA4 _atom_sites.fract_transf_matrix[1][1] 0.023583 _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] 0.018849 _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] 0.010785 _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 SE # 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 ARG 1 -3 ? ? ? A . n A 1 2 SER 2 -2 ? ? ? A . n A 1 3 PRO 3 -1 ? ? ? A . n A 1 4 TRP 4 0 ? ? ? A . n A 1 5 ASN 5 1 ? ? ? A . n A 1 6 ARG 6 2 ? ? ? A . n A 1 7 ILE 7 3 ? ? ? A . n A 1 8 PRO 8 4 ? ? ? A . n A 1 9 GLU 9 5 ? ? ? A . n A 1 10 SER 10 6 ? ? ? A . n A 1 11 GLY 11 7 ? ? ? A . n A 1 12 GLY 12 8 ? ? ? A . n A 1 13 ASP 13 9 ? ? ? A . n A 1 14 ASN 14 10 ? ? ? A . n A 1 15 SER 15 11 11 SER SER A . n A 1 16 VAL 16 12 12 VAL VAL A . n A 1 17 PHE 17 13 13 PHE PHE A . n A 1 18 ASP 18 14 14 ASP ASP A . n A 1 19 ILE 19 15 15 ILE ILE A . n A 1 20 PHE 20 16 16 PHE PHE A . n A 1 21 GLU 21 17 17 GLU GLU A . n A 1 22 LEU 22 18 18 LEU LEU A . n A 1 23 THR 23 19 19 THR THR A . n A 1 24 GLY 24 20 20 GLY GLY A . n A 1 25 ALA 25 21 21 ALA ALA A . n A 1 26 ALA 26 22 22 ALA ALA A . n A 1 27 ARG 27 23 23 ARG ARG A . n A 1 28 LYS 28 24 24 LYS LYS A . n A 1 29 GLY 29 25 25 GLY GLY A . n A 1 30 SER 30 26 26 SER SER A . n A 1 31 GLY 31 27 27 GLY GLY A . n A 1 32 ARG 32 28 28 ARG ARG A . n A 1 33 ARG 33 29 29 ARG ARG A . n A 1 34 LEU 34 30 30 LEU LEU A . n A 1 35 VAL 35 31 31 VAL VAL A . n A 1 36 LYS 36 32 32 LYS LYS A . n A 1 37 GLY 37 33 33 GLY GLY A . n A 1 38 PRO 38 34 34 PRO PRO A . n A 1 39 ASP 39 35 35 ASP ASP A . n A 1 40 PRO 40 36 36 PRO PRO A . n A 1 41 SER 41 37 37 SER SER A . n A 1 42 SER 42 38 38 SER SER A . n A 1 43 PRO 43 39 39 PRO PRO A . n A 1 44 ALA 44 40 40 ALA ALA A . n A 1 45 PHE 45 41 41 PHE PHE A . n A 1 46 ARG 46 42 42 ARG ARG A . n A 1 47 ILE 47 43 43 ILE ILE A . n A 1 48 GLU 48 44 44 GLU GLU A . n A 1 49 ASP 49 45 45 ASP ASP A . n A 1 50 ALA 50 46 46 ALA ALA A . n A 1 51 ASN 51 47 47 ASN ASN A . n A 1 52 LEU 52 48 48 LEU LEU A . n A 1 53 ILE 53 49 49 ILE ILE A . n A 1 54 PRO 54 50 50 PRO PRO A . n A 1 55 PRO 55 51 51 PRO PRO A . n A 1 56 VAL 56 52 52 VAL VAL A . n A 1 57 PRO 57 53 53 PRO PRO A . n A 1 58 ASP 58 54 54 ASP ASP A . n A 1 59 ASP 59 55 55 ASP ASP A . n A 1 60 LYS 60 56 56 LYS LYS A . n A 1 61 PHE 61 57 57 PHE PHE A . n A 1 62 GLN 62 58 58 GLN GLN A . n A 1 63 ASP 63 59 59 ASP ASP A . n A 1 64 LEU 64 60 60 LEU LEU A . n A 1 65 VAL 65 61 61 VAL VAL A . n A 1 66 ASP 66 62 62 ASP ASP A . n A 1 67 ALA 67 63 63 ALA ALA A . n A 1 68 VAL 68 64 64 VAL VAL A . n A 1 69 ARG 69 65 65 ARG ARG A . n A 1 70 THR 70 66 66 THR THR A . n A 1 71 GLU 71 67 67 GLU GLU A . n A 1 72 LYS 72 68 68 LYS LYS A . n A 1 73 GLY 73 69 69 GLY GLY A . n A 1 74 PHE 74 70 70 PHE PHE A . n A 1 75 LEU 75 71 71 LEU LEU A . n A 1 76 LEU 76 72 72 LEU LEU A . n A 1 77 LEU 77 73 73 LEU LEU A . n A 1 78 ALA 78 74 74 ALA ALA A . n A 1 79 SER 79 75 75 SER SER A . n A 1 80 LEU 80 76 76 LEU LEU A . n A 1 81 ARG 81 77 77 ARG ARG A . n A 1 82 GLN 82 78 78 GLN GLN A . n A 1 83 MSE 83 79 79 MSE MSE A . n A 1 84 LYS 84 80 80 LYS LYS A . n A 1 85 LYS 85 81 81 LYS LYS A . n A 1 86 THR 86 82 82 THR THR A . n A 1 87 ARG 87 83 83 ARG ARG A . n A 1 88 GLY 88 84 84 GLY GLY A . n A 1 89 THR 89 85 85 THR THR A . n A 1 90 LEU 90 86 86 LEU LEU A . n A 1 91 LEU 91 87 87 LEU LEU A . n A 1 92 ALA 92 88 88 ALA ALA A . n A 1 93 LEU 93 89 89 LEU LEU A . n A 1 94 GLU 94 90 90 GLU GLU A . n A 1 95 ARG 95 91 91 ARG ARG A . n A 1 96 LYS 96 92 92 LYS LYS A . n A 1 97 ASP 97 93 93 ASP ASP A . n A 1 98 HIS 98 94 94 HIS HIS A . n A 1 99 SER 99 95 95 SER SER A . n A 1 100 GLY 100 96 96 GLY GLY A . n A 1 101 GLN 101 97 97 GLN GLN A . n A 1 102 VAL 102 98 98 VAL VAL A . n A 1 103 PHE 103 99 99 PHE PHE A . n A 1 104 SER 104 100 100 SER SER A . n A 1 105 VAL 105 101 101 VAL VAL A . n A 1 106 VAL 106 102 102 VAL VAL A . n A 1 107 SER 107 103 103 SER SER A . n A 1 108 ASN 108 104 104 ASN ASN A . n A 1 109 GLY 109 105 105 GLY GLY A . n A 1 110 LYS 110 106 106 LYS LYS A . n A 1 111 ALA 111 107 107 ALA ALA A . n A 1 112 GLY 112 108 108 GLY GLY A . n A 1 113 THR 113 109 109 THR THR A . n A 1 114 LEU 114 110 110 LEU LEU A . n A 1 115 ASP 115 111 111 ASP ASP A . n A 1 116 LEU 116 112 112 LEU LEU A . n A 1 117 SER 117 113 113 SER SER A . n A 1 118 LEU 118 114 114 LEU LEU A . n A 1 119 THR 119 115 115 THR THR A . n A 1 120 VAL 120 116 116 VAL VAL A . n A 1 121 GLN 121 117 117 GLN GLN A . n A 1 122 GLY 122 118 118 GLY GLY A . n A 1 123 LYS 123 119 119 LYS LYS A . n A 1 124 GLN 124 120 120 GLN GLN A . n A 1 125 HIS 125 121 121 HIS HIS A . n A 1 126 VAL 126 122 122 VAL VAL A . n A 1 127 VAL 127 123 123 VAL VAL A . n A 1 128 SER 128 124 124 SER SER A . n A 1 129 VAL 129 125 125 VAL VAL A . n A 1 130 GLU 130 126 126 GLU GLU A . n A 1 131 GLU 131 127 127 GLU GLU A . n A 1 132 ALA 132 128 128 ALA ALA A . n A 1 133 LEU 133 129 129 LEU LEU A . n A 1 134 LEU 134 130 130 LEU LEU A . n A 1 135 ALA 135 131 131 ALA ALA A . n A 1 136 THR 136 132 132 THR THR A . n A 1 137 GLY 137 133 133 GLY GLY A . n A 1 138 GLN 138 134 134 GLN GLN A . n A 1 139 TRP 139 135 135 TRP TRP A . n A 1 140 LYS 140 136 136 LYS LYS A . n A 1 141 SER 141 137 137 SER SER A . n A 1 142 ILE 142 138 138 ILE ILE A . n A 1 143 THR 143 139 139 THR THR A . n A 1 144 LEU 144 140 140 LEU LEU A . n A 1 145 PHE 145 141 141 PHE PHE A . n A 1 146 VAL 146 142 142 VAL VAL A . n A 1 147 GLN 147 143 143 GLN GLN A . n A 1 148 GLU 148 144 144 GLU GLU A . n A 1 149 ASP 149 145 145 ASP ASP A . n A 1 150 ARG 150 146 146 ARG ARG A . n A 1 151 ALA 151 147 147 ALA ALA A . n A 1 152 GLN 152 148 148 GLN GLN A . n A 1 153 LEU 153 149 149 LEU LEU A . n A 1 154 TYR 154 150 150 TYR TYR A . n A 1 155 ILE 155 151 151 ILE ILE A . n A 1 156 ASP 156 152 152 ASP ASP A . n A 1 157 CYS 157 153 153 CYS CYS A . n A 1 158 GLU 158 154 154 GLU GLU A . n A 1 159 LYS 159 155 155 LYS LYS A . n A 1 160 MSE 160 156 156 MSE MSE A . n A 1 161 GLU 161 157 157 GLU GLU A . n A 1 162 ASN 162 158 158 ASN ASN A . n A 1 163 ALA 163 159 159 ALA ALA A . n A 1 164 GLU 164 160 160 GLU GLU A . n A 1 165 LEU 165 161 161 LEU LEU A . n A 1 166 ASP 166 162 162 ASP ASP A . n A 1 167 VAL 167 163 163 VAL VAL A . n A 1 168 PRO 168 164 164 PRO PRO A . n A 1 169 ILE 169 165 165 ILE ILE A . n A 1 170 GLN 170 166 166 GLN GLN A . n A 1 171 SER 171 167 167 SER SER A . n A 1 172 VAL 172 168 168 VAL VAL A . n A 1 173 PHE 173 169 169 PHE PHE A . n A 1 174 THR 174 170 170 THR THR A . n A 1 175 ARG 175 171 171 ARG ARG A . n A 1 176 ASP 176 172 172 ASP ASP A . n A 1 177 LEU 177 173 173 LEU LEU A . n A 1 178 ALA 178 174 174 ALA ALA A . n A 1 179 SER 179 175 175 SER SER A . n A 1 180 ILE 180 176 176 ILE ILE A . n A 1 181 ALA 181 177 177 ALA ALA A . n A 1 182 ARG 182 178 178 ARG ARG A . n A 1 183 LEU 183 179 179 LEU LEU A . n A 1 184 ARG 184 180 180 ARG ARG A . n A 1 185 ILE 185 181 181 ILE ILE A . n A 1 186 ALA 186 182 182 ALA ALA A . n A 1 187 LYS 187 183 183 LYS LYS A . n A 1 188 GLY 188 184 184 GLY GLY A . n A 1 189 GLY 189 185 185 GLY GLY A . n A 1 190 VAL 190 186 186 VAL VAL A . n A 1 191 ASN 191 187 187 ASN ASN A . n A 1 192 ASP 192 188 188 ASP ASP A . n A 1 193 ASN 193 189 189 ASN ASN A . n A 1 194 PHE 194 190 190 PHE PHE A . n A 1 195 GLN 195 191 191 GLN GLN A . n A 1 196 GLY 196 192 192 GLY GLY A . n A 1 197 VAL 197 193 193 VAL VAL A . n A 1 198 LEU 198 194 194 LEU LEU A . n A 1 199 GLN 199 195 195 GLN GLN A . n A 1 200 ASN 200 196 196 ASN ASN A . n A 1 201 VAL 201 197 197 VAL VAL A . n A 1 202 ARG 202 198 198 ARG ARG A . n A 1 203 PHE 203 199 199 PHE PHE A . n A 1 204 VAL 204 200 200 VAL VAL A . n A 1 205 PHE 205 201 201 PHE PHE A . n A 1 206 GLY 206 202 202 GLY GLY A . n A 1 207 THR 207 203 203 THR THR A . n A 1 208 THR 208 204 204 THR THR A . n A 1 209 PRO 209 205 205 PRO PRO A . n A 1 210 GLU 210 206 206 GLU GLU A . n A 1 211 ASP 211 207 207 ASP ASP A . n A 1 212 ILE 212 208 208 ILE ILE A . n A 1 213 LEU 213 209 209 LEU LEU A . n A 1 214 ARG 214 210 210 ARG ARG A . n A 1 215 ASN 215 211 211 ASN ASN A . n A 1 216 LYS 216 212 212 LYS LYS A . n A 1 217 GLY 217 213 213 GLY GLY A . n A 1 218 CYS 218 214 214 CYS CYS A . n A 1 219 SER 219 215 215 SER SER A . n A 1 220 SER 220 216 ? ? ? A . n A 1 221 SER 221 217 ? ? ? A . n A 1 222 THR 222 218 ? ? ? A . n A 1 223 SER 223 219 ? ? ? A . n A 1 224 VAL 224 220 ? ? ? A . n A 1 225 LEU 225 221 ? ? ? A . n A 1 226 LEU 226 222 ? ? ? A . n A 1 227 THR 227 223 ? ? ? A . n A 1 228 LEU 228 224 ? ? ? A . n A 1 229 ASP 229 225 ? ? ? A . n A 1 230 ASN 230 226 ? ? ? A . n A 1 231 ASN 231 227 ? ? ? A . n A 1 232 VAL 232 228 ? ? ? A . n A 1 233 VAL 233 229 ? ? ? A . n A 1 234 ASN 234 230 ? ? ? A . n A 1 235 GLY 235 231 ? ? ? A . n A 1 236 SER 236 232 ? ? ? A . n A 1 237 SER 237 233 ? ? ? A . n A 1 238 PRO 238 234 ? ? ? A . n A 1 239 ALA 239 235 ? ? ? A . n A 1 240 ILE 240 236 ? ? ? A . n A 1 241 ARG 241 237 ? ? ? A . n A 1 242 THR 242 238 ? ? ? A . n A 1 243 ASN 243 239 ? ? ? A . n A 1 244 THR 244 240 ? ? ? A . n A 1 245 GLY 245 241 ? ? ? A . n A 1 246 HIS 246 242 ? ? ? A . n A 1 247 HIS 247 243 ? ? ? A . n A 1 248 HIS 248 244 ? ? ? A . n A 1 249 HIS 249 245 ? ? ? A . n A 1 250 HIS 250 246 ? ? ? A . n A 1 251 HIS 251 247 ? ? ? 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 B 2 SGN 1 248 161 SGN SGN A . C 3 SO4 1 249 111 SO4 SO4 A . D 3 SO4 1 250 121 SO4 SO4 A . E 3 SO4 1 251 131 SO4 SO4 A . F 3 SO4 1 252 141 SO4 SO4 A . G 3 SO4 1 253 151 SO4 SO4 A . H 4 HOH 1 254 1 HOH HOH A . H 4 HOH 2 255 2 HOH HOH A . H 4 HOH 3 256 3 HOH HOH A . H 4 HOH 4 257 4 HOH HOH A . H 4 HOH 5 258 5 HOH HOH A . H 4 HOH 6 259 6 HOH HOH A . H 4 HOH 7 260 7 HOH HOH A . H 4 HOH 8 261 8 HOH HOH A . H 4 HOH 9 262 9 HOH HOH A . H 4 HOH 10 263 10 HOH HOH A . H 4 HOH 11 264 11 HOH HOH A . H 4 HOH 12 265 12 HOH HOH A . H 4 HOH 13 266 13 HOH HOH A . H 4 HOH 14 267 14 HOH HOH A . H 4 HOH 15 268 15 HOH HOH A . H 4 HOH 16 269 16 HOH HOH A . H 4 HOH 17 270 17 HOH HOH A . H 4 HOH 18 271 18 HOH HOH A . H 4 HOH 19 272 19 HOH HOH A . H 4 HOH 20 273 20 HOH HOH A . H 4 HOH 21 274 21 HOH HOH A . H 4 HOH 22 275 22 HOH HOH A . H 4 HOH 23 276 23 HOH HOH A . H 4 HOH 24 277 24 HOH HOH A . H 4 HOH 25 278 25 HOH HOH A . H 4 HOH 26 279 26 HOH HOH A . H 4 HOH 27 280 27 HOH HOH A . H 4 HOH 28 281 28 HOH HOH A . H 4 HOH 29 282 29 HOH HOH A . H 4 HOH 30 283 30 HOH HOH A . H 4 HOH 31 284 31 HOH HOH A . H 4 HOH 32 285 32 HOH HOH A . H 4 HOH 33 286 33 HOH HOH A . H 4 HOH 34 287 34 HOH HOH A . H 4 HOH 35 288 35 HOH HOH A . H 4 HOH 36 289 36 HOH HOH A . H 4 HOH 37 290 37 HOH HOH A . H 4 HOH 38 291 38 HOH HOH A . H 4 HOH 39 292 39 HOH HOH A . H 4 HOH 40 293 40 HOH HOH A . H 4 HOH 41 294 41 HOH HOH A . H 4 HOH 42 295 42 HOH HOH A . H 4 HOH 43 296 43 HOH HOH A . H 4 HOH 44 297 44 HOH HOH A . H 4 HOH 45 298 45 HOH HOH A . H 4 HOH 46 299 46 HOH HOH A . H 4 HOH 47 300 47 HOH HOH A . H 4 HOH 48 301 48 HOH HOH A . H 4 HOH 49 302 49 HOH HOH A . H 4 HOH 50 303 50 HOH HOH A . H 4 HOH 51 304 51 HOH HOH A . H 4 HOH 52 305 52 HOH HOH A . H 4 HOH 53 306 53 HOH HOH A . H 4 HOH 54 307 54 HOH HOH A . H 4 HOH 55 308 55 HOH HOH A . H 4 HOH 56 309 56 HOH HOH A . H 4 HOH 57 310 57 HOH HOH A . H 4 HOH 58 311 58 HOH HOH A . H 4 HOH 59 312 59 HOH HOH A . H 4 HOH 60 313 60 HOH HOH A . H 4 HOH 61 314 61 HOH HOH A . H 4 HOH 62 315 62 HOH HOH A . H 4 HOH 63 316 63 HOH HOH A . H 4 HOH 64 317 64 HOH HOH A . H 4 HOH 65 318 65 HOH HOH A . H 4 HOH 66 319 66 HOH HOH A . H 4 HOH 67 320 67 HOH HOH A . H 4 HOH 68 321 68 HOH HOH A . H 4 HOH 69 322 69 HOH HOH A . H 4 HOH 70 323 70 HOH HOH A . H 4 HOH 71 324 71 HOH HOH A . H 4 HOH 72 325 72 HOH HOH A . H 4 HOH 73 326 73 HOH HOH A . H 4 HOH 74 327 74 HOH HOH A . H 4 HOH 75 328 75 HOH HOH A . H 4 HOH 76 329 76 HOH HOH A . H 4 HOH 77 330 77 HOH HOH A . H 4 HOH 78 331 78 HOH HOH 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 MSE 83 A MSE 79 ? MET SELENOMETHIONINE 2 A MSE 160 A MSE 156 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 2006-01-24 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 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 4 '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' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 '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' entity 4 4 'Structure model' pdbx_chem_comp_identifier 5 4 'Structure model' pdbx_entity_nonpoly 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_ref_seq_dif 8 4 'Structure model' struct_site 9 4 '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' '_atom_site.auth_atom_id' 2 4 'Structure model' '_atom_site.label_atom_id' 3 4 'Structure model' '_chem_comp.mon_nstd_flag' 4 4 'Structure model' '_chem_comp.name' 5 4 'Structure model' '_chem_comp.type' 6 4 'Structure model' '_entity.pdbx_description' 7 4 'Structure model' '_pdbx_entity_nonpoly.name' 8 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 9 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 HKL-2000 'data reduction' . ? 2 MLPHARE phasing . ? 3 CNS refinement 1.1 ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ARIXTRA MOLECULE WAS NOT OBSERVED. SGN, N,O6-DISULFO-GLUCOSAMINE IS PART OF ARIXTRA MOLECULE (DEFINED AS FIFTH UNIT) AND SO4, SULFATE IONS ARE ALSO PART OF ARIXTRA MOLECULE (FRAGMENTS FROM THE REST OF THE UNITS). ; # 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 ASP A 45 ? ? -160.55 92.08 2 1 GLU A 144 ? ? 63.58 -119.53 3 1 ASP A 152 ? ? 62.17 -110.03 # 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 ARG -3 ? A ARG 1 2 1 Y 1 A SER -2 ? A SER 2 3 1 Y 1 A PRO -1 ? A PRO 3 4 1 Y 1 A TRP 0 ? A TRP 4 5 1 Y 1 A ASN 1 ? A ASN 5 6 1 Y 1 A ARG 2 ? A ARG 6 7 1 Y 1 A ILE 3 ? A ILE 7 8 1 Y 1 A PRO 4 ? A PRO 8 9 1 Y 1 A GLU 5 ? A GLU 9 10 1 Y 1 A SER 6 ? A SER 10 11 1 Y 1 A GLY 7 ? A GLY 11 12 1 Y 1 A GLY 8 ? A GLY 12 13 1 Y 1 A ASP 9 ? A ASP 13 14 1 Y 1 A ASN 10 ? A ASN 14 15 1 Y 1 A SER 216 ? A SER 220 16 1 Y 1 A SER 217 ? A SER 221 17 1 Y 1 A THR 218 ? A THR 222 18 1 Y 1 A SER 219 ? A SER 223 19 1 Y 1 A VAL 220 ? A VAL 224 20 1 Y 1 A LEU 221 ? A LEU 225 21 1 Y 1 A LEU 222 ? A LEU 226 22 1 Y 1 A THR 223 ? A THR 227 23 1 Y 1 A LEU 224 ? A LEU 228 24 1 Y 1 A ASP 225 ? A ASP 229 25 1 Y 1 A ASN 226 ? A ASN 230 26 1 Y 1 A ASN 227 ? A ASN 231 27 1 Y 1 A VAL 228 ? A VAL 232 28 1 Y 1 A VAL 229 ? A VAL 233 29 1 Y 1 A ASN 230 ? A ASN 234 30 1 Y 1 A GLY 231 ? A GLY 235 31 1 Y 1 A SER 232 ? A SER 236 32 1 Y 1 A SER 233 ? A SER 237 33 1 Y 1 A PRO 234 ? A PRO 238 34 1 Y 1 A ALA 235 ? A ALA 239 35 1 Y 1 A ILE 236 ? A ILE 240 36 1 Y 1 A ARG 237 ? A ARG 241 37 1 Y 1 A THR 238 ? A THR 242 38 1 Y 1 A ASN 239 ? A ASN 243 39 1 Y 1 A THR 240 ? A THR 244 40 1 Y 1 A GLY 241 ? A GLY 245 41 1 Y 1 A HIS 242 ? A HIS 246 42 1 Y 1 A HIS 243 ? A HIS 247 43 1 Y 1 A HIS 244 ? A HIS 248 44 1 Y 1 A HIS 245 ? A HIS 249 45 1 Y 1 A HIS 246 ? A HIS 250 46 1 Y 1 A HIS 247 ? A HIS 251 # 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 SGN 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 'DGlcpNS[6S]a' SGN 'COMMON NAME' GMML 1.0 N-sulfo-6-sulfo-a-D-glucopyranose SGN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GlcpNSO36SO3 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose' SGN 3 'SULFATE ION' SO4 4 water HOH #