data_4BSJ # _entry.id 4BSJ # _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 4BSJ PDBE EBI-56514 WWPDB D_1290056514 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4BSK _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH VEGFR-3 DOMAINS D1-2' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4BSJ _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2013-06-10 _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 'Leppanen, V.-M.' 1 'Tvorogov, D.' 2 'Kisko, K.' 3 'Prota, A.E.' 4 'Jeltsch, M.' 5 'Anisimov, A.' 6 'Markovic-Mueller, S.' 7 'Stuttfeld, E.' 8 'Goldie, K.N.' 9 'Ballmer-Hofer, K.' 10 'Alitalo, K.' 11 # _citation.id primary _citation.title 'Structural and Mechanistic Insights Into Vegfr-3 Ligand Binding and Activation' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 110 _citation.page_first 12960 _citation.page_last ? _citation.year 2013 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23878260 _citation.pdbx_database_id_DOI 10.1073/PNAS.1301415110 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Leppanen, V.-M.' 1 ? primary 'Tvorogov, D.' 2 ? primary 'Kisko, K.' 3 ? primary 'Prota, A.E.' 4 ? primary 'Jeltsch, M.' 5 ? primary 'Anisimov, A.' 6 ? primary 'Markovic-Mueller, S.' 7 ? primary 'Stuttfeld, E.' 8 ? primary 'Goldie, K.N.' 9 ? primary 'Ballmer-Hofer, K.' 10 ? primary 'Alitalo, K.' 11 ? # _cell.entry_id 4BSJ _cell.length_a 133.340 _cell.length_b 133.340 _cell.length_c 48.930 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BSJ _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 # 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 'VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3' 26521.211 1 2.7.10.1 ? 'EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553' ? 2 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? 3 water nat water 18.015 21 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'VEGFR-3, FMS-LIKE TYROSINE KINASE 4, FLT-4, TYROSINE-PROTEIN KINASE RECEPTOR FLT4, VEGFR-3' # _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 ;DHNPFISVEWLKGPILEATAGDELVKLPVKLAAYPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAG LRRNISLELVVNVPPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQDLMPQCR DWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKVGQDERLIYFYVTTHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;DHNPFISVEWLKGPILEATAGDELVKLPVKLAAYPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAG LRRNISLELVVNVPPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQDLMPQCR DWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKVGQDERLIYFYVTTHHHHHH ; _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 ASP n 1 2 HIS n 1 3 ASN n 1 4 PRO n 1 5 PHE n 1 6 ILE n 1 7 SER n 1 8 VAL n 1 9 GLU n 1 10 TRP n 1 11 LEU n 1 12 LYS n 1 13 GLY n 1 14 PRO n 1 15 ILE n 1 16 LEU n 1 17 GLU n 1 18 ALA n 1 19 THR n 1 20 ALA n 1 21 GLY n 1 22 ASP n 1 23 GLU n 1 24 LEU n 1 25 VAL n 1 26 LYS n 1 27 LEU n 1 28 PRO n 1 29 VAL n 1 30 LYS n 1 31 LEU n 1 32 ALA n 1 33 ALA n 1 34 TYR n 1 35 PRO n 1 36 PRO n 1 37 PRO n 1 38 GLU n 1 39 PHE n 1 40 GLN n 1 41 TRP n 1 42 TYR n 1 43 LYS n 1 44 ASP n 1 45 GLY n 1 46 LYS n 1 47 ALA n 1 48 LEU n 1 49 SER n 1 50 GLY n 1 51 ARG n 1 52 HIS n 1 53 SER n 1 54 PRO n 1 55 HIS n 1 56 ALA n 1 57 LEU n 1 58 VAL n 1 59 LEU n 1 60 LYS n 1 61 GLU n 1 62 VAL n 1 63 THR n 1 64 GLU n 1 65 ALA n 1 66 SER n 1 67 THR n 1 68 GLY n 1 69 THR n 1 70 TYR n 1 71 THR n 1 72 LEU n 1 73 ALA n 1 74 LEU n 1 75 TRP n 1 76 ASN n 1 77 SER n 1 78 ALA n 1 79 ALA n 1 80 GLY n 1 81 LEU n 1 82 ARG n 1 83 ARG n 1 84 ASN n 1 85 ILE n 1 86 SER n 1 87 LEU n 1 88 GLU n 1 89 LEU n 1 90 VAL n 1 91 VAL n 1 92 ASN n 1 93 VAL n 1 94 PRO n 1 95 PRO n 1 96 GLN n 1 97 ILE n 1 98 HIS n 1 99 GLU n 1 100 LYS n 1 101 GLU n 1 102 ALA n 1 103 SER n 1 104 SER n 1 105 PRO n 1 106 SER n 1 107 ILE n 1 108 TYR n 1 109 SER n 1 110 ARG n 1 111 HIS n 1 112 SER n 1 113 ARG n 1 114 GLN n 1 115 ALA n 1 116 LEU n 1 117 THR n 1 118 CYS n 1 119 THR n 1 120 ALA n 1 121 TYR n 1 122 GLY n 1 123 VAL n 1 124 PRO n 1 125 LEU n 1 126 PRO n 1 127 LEU n 1 128 SER n 1 129 ILE n 1 130 GLN n 1 131 TRP n 1 132 HIS n 1 133 TRP n 1 134 ARG n 1 135 PRO n 1 136 TRP n 1 137 THR n 1 138 PRO n 1 139 CYS n 1 140 LYS n 1 141 MET n 1 142 PHE n 1 143 ALA n 1 144 GLN n 1 145 ARG n 1 146 SER n 1 147 LEU n 1 148 ARG n 1 149 ARG n 1 150 ARG n 1 151 GLN n 1 152 GLN n 1 153 GLN n 1 154 ASP n 1 155 LEU n 1 156 MET n 1 157 PRO n 1 158 GLN n 1 159 CYS n 1 160 ARG n 1 161 ASP n 1 162 TRP n 1 163 ARG n 1 164 ALA n 1 165 VAL n 1 166 THR n 1 167 THR n 1 168 GLN n 1 169 ASP n 1 170 ALA n 1 171 VAL n 1 172 ASN n 1 173 PRO n 1 174 ILE n 1 175 GLU n 1 176 SER n 1 177 LEU n 1 178 ASP n 1 179 THR n 1 180 TRP n 1 181 THR n 1 182 GLU n 1 183 PHE n 1 184 VAL n 1 185 GLU n 1 186 GLY n 1 187 LYS n 1 188 ASN n 1 189 LYS n 1 190 THR n 1 191 VAL n 1 192 SER n 1 193 LYS n 1 194 LEU n 1 195 VAL n 1 196 ILE n 1 197 GLN n 1 198 ASN n 1 199 ALA n 1 200 ASN n 1 201 VAL n 1 202 SER n 1 203 ALA n 1 204 MET n 1 205 TYR n 1 206 LYS n 1 207 CYS n 1 208 VAL n 1 209 VAL n 1 210 SER n 1 211 ASN n 1 212 LYS n 1 213 VAL n 1 214 GLY n 1 215 GLN n 1 216 ASP n 1 217 GLU n 1 218 ARG n 1 219 LEU n 1 220 ILE n 1 221 TYR n 1 222 PHE n 1 223 TYR n 1 224 VAL n 1 225 THR n 1 226 THR n 1 227 HIS n 1 228 HIS n 1 229 HIS n 1 230 HIS n 1 231 HIS n 1 232 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 ? _entity_src_gen.pdbx_gene_src_gene ? _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 'FALL ARMYWORM' _entity_src_gen.pdbx_host_org_scientific_name 'SPODOPTERA FRUGIPERDA' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7108 _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 Sf21 _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 BACULOVIRUS _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PFASTBAC1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code VGFR3_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P35916 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4BSJ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 226 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P35916 _struct_ref_seq.db_align_beg 330 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 553 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 330 _struct_ref_seq.pdbx_auth_seq_align_end 553 # 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 4BSJ ASP A 1 ? UNP P35916 ? ? 'cloning artifact' 328 1 1 4BSJ HIS A 2 ? UNP P35916 ? ? 'cloning artifact' 329 2 1 4BSJ HIS A 227 ? UNP P35916 ? ? 'expression tag' 554 3 1 4BSJ HIS A 228 ? UNP P35916 ? ? 'expression tag' 555 4 1 4BSJ HIS A 229 ? UNP P35916 ? ? 'expression tag' 556 5 1 4BSJ HIS A 230 ? UNP P35916 ? ? 'expression tag' 557 6 1 4BSJ HIS A 231 ? UNP P35916 ? ? 'expression tag' 558 7 1 4BSJ HIS A 232 ? UNP P35916 ? ? 'expression tag' 559 8 # 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 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 4BSJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.74 _exptl_crystal.density_percent_sol 74.1 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%.' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2011-04-09 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI(111) MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06SA _diffrn_source.pdbx_wavelength 1.00 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4BSJ _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.00 _reflns.d_resolution_high 2.50 _reflns.number_obs 17532 _reflns.number_all ? _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 28.10 _reflns.B_iso_Wilson_estimate 73.0 _reflns.pdbx_redundancy 9.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.65 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 1.32 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.20 _reflns_shell.pdbx_redundancy 10.3 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4BSJ _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 17525 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.99 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.492 _refine.ls_d_res_high 2.500 _refine.ls_percent_reflns_obs 99.82 _refine.ls_R_factor_obs 0.2118 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2098 _refine.ls_R_factor_R_free 0.2533 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 878 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 61.2 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ;AN INITIAL MODEL WAS BUILT WITH ARPWARP AND REFINED WITH REFMAC. RESIDUES 470-483 AND SIDECHAINS OF RESIDUES 328, 329, 469, 485 AND 487 ARE DISORDERED AND WERE OMITTED FROM THE FINAL MODEL. ; _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct SIRAS _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.33 _refine.pdbx_overall_phase_error 28.74 _refine.overall_SU_B ? _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 1673 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 21 _refine_hist.number_atoms_total 1722 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 38.492 # 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 f_bond_d 0.006 ? ? 1753 'X-RAY DIFFRACTION' ? f_angle_d 1.021 ? ? 2396 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 13.566 ? ? 633 'X-RAY DIFFRACTION' ? f_chiral_restr 0.066 ? ? 274 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 297 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.5000 2.6567 2746 0.3115 100.00 0.3380 . . 142 . . 'X-RAY DIFFRACTION' . 2.6567 2.8617 2746 0.2964 100.00 0.3072 . . 135 . . 'X-RAY DIFFRACTION' . 2.8617 3.1496 2746 0.2642 100.00 0.3149 . . 155 . . 'X-RAY DIFFRACTION' . 3.1496 3.6050 2738 0.2291 100.00 0.2623 . . 172 . . 'X-RAY DIFFRACTION' . 3.6050 4.5408 2790 0.1925 100.00 0.2190 . . 140 . . 'X-RAY DIFFRACTION' . 4.5408 38.4965 2881 0.1825 100.00 0.2421 . . 134 . . # _struct.entry_id 4BSJ _struct.title 'Crystal structure of VEGFR-3 extracellular domains D4-5' _struct.pdbx_descriptor 'VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 (E.C.2.7.10.1)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4BSJ _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'TRANSFERASE, LYMPHANGIOGENESIS, ANGIOGENESIS, VASCULAR, IG DOMAIN, GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, DIMERIZATION' # 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 2 ? D N N 3 ? # 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 AA1 THR A 63 ? THR A 67 ? THR A 390 THR A 394 5 ? 5 HELX_P HELX_P2 AA2 GLU A 99 ? ALA A 102 ? GLU A 426 ALA A 429 5 ? 4 # _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 118 SG ? ? ? 1_555 A CYS 207 SG ? ? A CYS 445 A CYS 534 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf2 disulf ? ? A CYS 139 SG ? ? ? 1_555 A CYS 159 SG ? ? A CYS 466 A CYS 486 1_555 ? ? ? ? ? ? ? 2.036 ? ? covale1 covale one ? A ASN 84 ND2 ? ? ? 1_555 B NAG . C1 ? ? A ASN 411 A NAG 601 1_555 ? ? ? ? ? ? ? 1.445 ? N-Glycosylation covale2 covale one ? A ASN 188 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 515 A NAG 602 1_555 ? ? ? ? ? ? ? 1.444 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLY 13 A . ? GLY 340 A PRO 14 A ? PRO 341 A 1 -7.80 2 TYR 34 A . ? TYR 361 A PRO 35 A ? PRO 362 A 1 -5.77 3 VAL 123 A . ? VAL 450 A PRO 124 A ? PRO 451 A 1 -1.25 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 5 ? AA3 ? 5 ? AA4 ? 2 ? AA5 ? 4 ? # 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 AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA2 1 2 ? parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA3 1 2 ? parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA3 4 5 ? anti-parallel AA4 1 2 ? parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA5 3 4 ? 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 AA1 1 PHE A 5 ? TRP A 10 ? PHE A 332 TRP A 337 AA1 2 GLU A 23 ? TYR A 34 ? GLU A 350 TYR A 361 AA1 3 ALA A 56 ? GLU A 61 ? ALA A 383 GLU A 388 AA2 1 ILE A 15 ? THR A 19 ? ILE A 342 THR A 346 AA2 2 LEU A 81 ? ILE A 97 ? LEU A 408 ILE A 424 AA2 3 GLY A 68 ? ASN A 76 ? GLY A 395 ASN A 403 AA2 4 GLU A 38 ? LYS A 43 ? GLU A 365 LYS A 370 AA2 5 LYS A 46 ? ALA A 47 ? LYS A 373 ALA A 374 AA3 1 ILE A 15 ? THR A 19 ? ILE A 342 THR A 346 AA3 2 LEU A 81 ? ILE A 97 ? LEU A 408 ILE A 424 AA3 3 GLN A 114 ? VAL A 123 ? GLN A 441 VAL A 450 AA3 4 LYS A 187 ? ILE A 196 ? LYS A 514 ILE A 523 AA3 5 ILE A 174 ? VAL A 184 ? ILE A 501 VAL A 511 AA4 1 TYR A 108 ? SER A 109 ? TYR A 435 SER A 436 AA4 2 VAL A 224 ? THR A 225 ? VAL A 551 THR A 552 AA5 1 ARG A 163 ? ALA A 164 ? ARG A 490 ALA A 491 AA5 2 GLN A 130 ? PRO A 135 ? GLN A 457 PRO A 462 AA5 3 ALA A 203 ? ASN A 211 ? ALA A 530 ASN A 538 AA5 4 GLY A 214 ? PHE A 222 ? GLY A 541 PHE A 549 # 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 AA1 1 2 N GLU A 9 ? N GLU A 336 O LYS A 30 ? O LYS A 357 AA1 2 3 N VAL A 25 ? N VAL A 352 O LEU A 59 ? O LEU A 386 AA2 1 2 N LEU A 16 ? N LEU A 343 O GLU A 88 ? O GLU A 415 AA2 2 3 O LEU A 87 ? O LEU A 414 N TYR A 70 ? N TYR A 397 AA2 3 4 O ALA A 73 ? O ALA A 400 N GLN A 40 ? N GLN A 367 AA2 4 5 N LYS A 43 ? N LYS A 370 O LYS A 46 ? O LYS A 373 AA3 1 2 N LEU A 16 ? N LEU A 343 O GLU A 88 ? O GLU A 415 AA3 2 3 N VAL A 93 ? N VAL A 420 O VAL A 123 ? O VAL A 450 AA3 3 4 N ALA A 120 ? N ALA A 447 O THR A 190 ? O THR A 517 AA3 4 5 O LYS A 187 ? O LYS A 514 N VAL A 184 ? N VAL A 511 AA4 1 2 N TYR A 108 ? N TYR A 435 O THR A 225 ? O THR A 552 AA5 1 2 O ARG A 163 ? O ARG A 490 N TRP A 133 ? N TRP A 460 AA5 2 3 N ARG A 134 ? N ARG A 461 O MET A 204 ? O MET A 531 AA5 3 4 N TYR A 205 ? N TYR A 532 O ILE A 220 ? O ILE A 547 # _database_PDB_matrix.entry_id 4BSJ _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 4BSJ _atom_sites.fract_transf_matrix[1][1] 0.007500 _atom_sites.fract_transf_matrix[1][2] 0.004330 _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] 0.008660 _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] 0.020437 _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_ _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 ASP 1 328 328 ASP ASP A . n A 1 2 HIS 2 329 329 HIS HIS A . n A 1 3 ASN 3 330 330 ASN ASN A . n A 1 4 PRO 4 331 331 PRO PRO A . n A 1 5 PHE 5 332 332 PHE PHE A . n A 1 6 ILE 6 333 333 ILE ILE A . n A 1 7 SER 7 334 334 SER SER A . n A 1 8 VAL 8 335 335 VAL VAL A . n A 1 9 GLU 9 336 336 GLU GLU A . n A 1 10 TRP 10 337 337 TRP TRP A . n A 1 11 LEU 11 338 338 LEU LEU A . n A 1 12 LYS 12 339 339 LYS LYS A . n A 1 13 GLY 13 340 340 GLY GLY A . n A 1 14 PRO 14 341 341 PRO PRO A . n A 1 15 ILE 15 342 342 ILE ILE A . n A 1 16 LEU 16 343 343 LEU LEU A . n A 1 17 GLU 17 344 344 GLU GLU A . n A 1 18 ALA 18 345 345 ALA ALA A . n A 1 19 THR 19 346 346 THR THR A . n A 1 20 ALA 20 347 347 ALA ALA A . n A 1 21 GLY 21 348 348 GLY GLY A . n A 1 22 ASP 22 349 349 ASP ASP A . n A 1 23 GLU 23 350 350 GLU GLU A . n A 1 24 LEU 24 351 351 LEU LEU A . n A 1 25 VAL 25 352 352 VAL VAL A . n A 1 26 LYS 26 353 353 LYS LYS A . n A 1 27 LEU 27 354 354 LEU LEU A . n A 1 28 PRO 28 355 355 PRO PRO A . n A 1 29 VAL 29 356 356 VAL VAL A . n A 1 30 LYS 30 357 357 LYS LYS A . n A 1 31 LEU 31 358 358 LEU LEU A . n A 1 32 ALA 32 359 359 ALA ALA A . n A 1 33 ALA 33 360 360 ALA ALA A . n A 1 34 TYR 34 361 361 TYR TYR A . n A 1 35 PRO 35 362 362 PRO PRO A . n A 1 36 PRO 36 363 363 PRO PRO A . n A 1 37 PRO 37 364 364 PRO PRO A . n A 1 38 GLU 38 365 365 GLU GLU A . n A 1 39 PHE 39 366 366 PHE PHE A . n A 1 40 GLN 40 367 367 GLN GLN A . n A 1 41 TRP 41 368 368 TRP TRP A . n A 1 42 TYR 42 369 369 TYR TYR A . n A 1 43 LYS 43 370 370 LYS LYS A . n A 1 44 ASP 44 371 371 ASP ASP A . n A 1 45 GLY 45 372 372 GLY GLY A . n A 1 46 LYS 46 373 373 LYS LYS A . n A 1 47 ALA 47 374 374 ALA ALA A . n A 1 48 LEU 48 375 375 LEU LEU A . n A 1 49 SER 49 376 376 SER SER A . n A 1 50 GLY 50 377 377 GLY GLY A . n A 1 51 ARG 51 378 378 ARG ARG A . n A 1 52 HIS 52 379 379 HIS HIS A . n A 1 53 SER 53 380 380 SER SER A . n A 1 54 PRO 54 381 381 PRO PRO A . n A 1 55 HIS 55 382 382 HIS HIS A . n A 1 56 ALA 56 383 383 ALA ALA A . n A 1 57 LEU 57 384 384 LEU LEU A . n A 1 58 VAL 58 385 385 VAL VAL A . n A 1 59 LEU 59 386 386 LEU LEU A . n A 1 60 LYS 60 387 387 LYS LYS A . n A 1 61 GLU 61 388 388 GLU GLU A . n A 1 62 VAL 62 389 389 VAL VAL A . n A 1 63 THR 63 390 390 THR THR A . n A 1 64 GLU 64 391 391 GLU GLU A . n A 1 65 ALA 65 392 392 ALA ALA A . n A 1 66 SER 66 393 393 SER SER A . n A 1 67 THR 67 394 394 THR THR A . n A 1 68 GLY 68 395 395 GLY GLY A . n A 1 69 THR 69 396 396 THR THR A . n A 1 70 TYR 70 397 397 TYR TYR A . n A 1 71 THR 71 398 398 THR THR A . n A 1 72 LEU 72 399 399 LEU LEU A . n A 1 73 ALA 73 400 400 ALA ALA A . n A 1 74 LEU 74 401 401 LEU LEU A . n A 1 75 TRP 75 402 402 TRP TRP A . n A 1 76 ASN 76 403 403 ASN ASN A . n A 1 77 SER 77 404 404 SER SER A . n A 1 78 ALA 78 405 405 ALA ALA A . n A 1 79 ALA 79 406 406 ALA ALA A . n A 1 80 GLY 80 407 407 GLY GLY A . n A 1 81 LEU 81 408 408 LEU LEU A . n A 1 82 ARG 82 409 409 ARG ARG A . n A 1 83 ARG 83 410 410 ARG ARG A . n A 1 84 ASN 84 411 411 ASN ASN A . n A 1 85 ILE 85 412 412 ILE ILE A . n A 1 86 SER 86 413 413 SER SER A . n A 1 87 LEU 87 414 414 LEU LEU A . n A 1 88 GLU 88 415 415 GLU GLU A . n A 1 89 LEU 89 416 416 LEU LEU A . n A 1 90 VAL 90 417 417 VAL VAL A . n A 1 91 VAL 91 418 418 VAL VAL A . n A 1 92 ASN 92 419 419 ASN ASN A . n A 1 93 VAL 93 420 420 VAL VAL A . n A 1 94 PRO 94 421 421 PRO PRO A . n A 1 95 PRO 95 422 422 PRO PRO A . n A 1 96 GLN 96 423 423 GLN GLN A . n A 1 97 ILE 97 424 424 ILE ILE A . n A 1 98 HIS 98 425 425 HIS HIS A . n A 1 99 GLU 99 426 426 GLU GLU A . n A 1 100 LYS 100 427 427 LYS LYS A . n A 1 101 GLU 101 428 428 GLU GLU A . n A 1 102 ALA 102 429 429 ALA ALA A . n A 1 103 SER 103 430 430 SER SER A . n A 1 104 SER 104 431 431 SER SER A . n A 1 105 PRO 105 432 432 PRO PRO A . n A 1 106 SER 106 433 433 SER SER A . n A 1 107 ILE 107 434 434 ILE ILE A . n A 1 108 TYR 108 435 435 TYR TYR A . n A 1 109 SER 109 436 436 SER SER A . n A 1 110 ARG 110 437 437 ARG ARG A . n A 1 111 HIS 111 438 438 HIS HIS A . n A 1 112 SER 112 439 439 SER SER A . n A 1 113 ARG 113 440 440 ARG ARG A . n A 1 114 GLN 114 441 441 GLN GLN A . n A 1 115 ALA 115 442 442 ALA ALA A . n A 1 116 LEU 116 443 443 LEU LEU A . n A 1 117 THR 117 444 444 THR THR A . n A 1 118 CYS 118 445 445 CYS CYS A . n A 1 119 THR 119 446 446 THR THR A . n A 1 120 ALA 120 447 447 ALA ALA A . n A 1 121 TYR 121 448 448 TYR TYR A . n A 1 122 GLY 122 449 449 GLY GLY A . n A 1 123 VAL 123 450 450 VAL VAL A . n A 1 124 PRO 124 451 451 PRO PRO A . n A 1 125 LEU 125 452 452 LEU LEU A . n A 1 126 PRO 126 453 453 PRO PRO A . n A 1 127 LEU 127 454 454 LEU LEU A . n A 1 128 SER 128 455 455 SER SER A . n A 1 129 ILE 129 456 456 ILE ILE A . n A 1 130 GLN 130 457 457 GLN GLN A . n A 1 131 TRP 131 458 458 TRP TRP A . n A 1 132 HIS 132 459 459 HIS HIS A . n A 1 133 TRP 133 460 460 TRP TRP A . n A 1 134 ARG 134 461 461 ARG ARG A . n A 1 135 PRO 135 462 462 PRO PRO A . n A 1 136 TRP 136 463 463 TRP TRP A . n A 1 137 THR 137 464 464 THR THR A . n A 1 138 PRO 138 465 465 PRO PRO A . n A 1 139 CYS 139 466 466 CYS CYS A . n A 1 140 LYS 140 467 467 LYS LYS A . n A 1 141 MET 141 468 468 MET MET A . n A 1 142 PHE 142 469 469 PHE PHE A . n A 1 143 ALA 143 470 ? ? ? A . n A 1 144 GLN 144 471 ? ? ? A . n A 1 145 ARG 145 472 ? ? ? A . n A 1 146 SER 146 473 ? ? ? A . n A 1 147 LEU 147 474 ? ? ? A . n A 1 148 ARG 148 475 ? ? ? A . n A 1 149 ARG 149 476 ? ? ? A . n A 1 150 ARG 150 477 ? ? ? A . n A 1 151 GLN 151 478 ? ? ? A . n A 1 152 GLN 152 479 ? ? ? A . n A 1 153 GLN 153 480 ? ? ? A . n A 1 154 ASP 154 481 ? ? ? A . n A 1 155 LEU 155 482 ? ? ? A . n A 1 156 MET 156 483 ? ? ? A . n A 1 157 PRO 157 484 484 PRO PRO A . n A 1 158 GLN 158 485 485 GLN GLN A . n A 1 159 CYS 159 486 486 CYS CYS A . n A 1 160 ARG 160 487 487 ARG ARG A . n A 1 161 ASP 161 488 488 ASP ASP A . n A 1 162 TRP 162 489 489 TRP TRP A . n A 1 163 ARG 163 490 490 ARG ARG A . n A 1 164 ALA 164 491 491 ALA ALA A . n A 1 165 VAL 165 492 492 VAL VAL A . n A 1 166 THR 166 493 493 THR THR A . n A 1 167 THR 167 494 494 THR THR A . n A 1 168 GLN 168 495 495 GLN GLN A . n A 1 169 ASP 169 496 496 ASP ASP A . n A 1 170 ALA 170 497 497 ALA ALA A . n A 1 171 VAL 171 498 498 VAL VAL A . n A 1 172 ASN 172 499 499 ASN ASN A . n A 1 173 PRO 173 500 500 PRO PRO A . n A 1 174 ILE 174 501 501 ILE ILE A . n A 1 175 GLU 175 502 502 GLU GLU A . n A 1 176 SER 176 503 503 SER SER A . n A 1 177 LEU 177 504 504 LEU LEU A . n A 1 178 ASP 178 505 505 ASP ASP A . n A 1 179 THR 179 506 506 THR THR A . n A 1 180 TRP 180 507 507 TRP TRP A . n A 1 181 THR 181 508 508 THR THR A . n A 1 182 GLU 182 509 509 GLU GLU A . n A 1 183 PHE 183 510 510 PHE PHE A . n A 1 184 VAL 184 511 511 VAL VAL A . n A 1 185 GLU 185 512 512 GLU GLU A . n A 1 186 GLY 186 513 513 GLY GLY A . n A 1 187 LYS 187 514 514 LYS LYS A . n A 1 188 ASN 188 515 515 ASN ASN A . n A 1 189 LYS 189 516 516 LYS LYS A . n A 1 190 THR 190 517 517 THR THR A . n A 1 191 VAL 191 518 518 VAL VAL A . n A 1 192 SER 192 519 519 SER SER A . n A 1 193 LYS 193 520 520 LYS LYS A . n A 1 194 LEU 194 521 521 LEU LEU A . n A 1 195 VAL 195 522 522 VAL VAL A . n A 1 196 ILE 196 523 523 ILE ILE A . n A 1 197 GLN 197 524 524 GLN GLN A . n A 1 198 ASN 198 525 525 ASN ASN A . n A 1 199 ALA 199 526 526 ALA ALA A . n A 1 200 ASN 200 527 527 ASN ASN A . n A 1 201 VAL 201 528 528 VAL VAL A . n A 1 202 SER 202 529 529 SER SER A . n A 1 203 ALA 203 530 530 ALA ALA A . n A 1 204 MET 204 531 531 MET MET A . n A 1 205 TYR 205 532 532 TYR TYR A . n A 1 206 LYS 206 533 533 LYS LYS A . n A 1 207 CYS 207 534 534 CYS CYS A . n A 1 208 VAL 208 535 535 VAL VAL A . n A 1 209 VAL 209 536 536 VAL VAL A . n A 1 210 SER 210 537 537 SER SER A . n A 1 211 ASN 211 538 538 ASN ASN A . n A 1 212 LYS 212 539 539 LYS LYS A . n A 1 213 VAL 213 540 540 VAL VAL A . n A 1 214 GLY 214 541 541 GLY GLY A . n A 1 215 GLN 215 542 542 GLN GLN A . n A 1 216 ASP 216 543 543 ASP ASP A . n A 1 217 GLU 217 544 544 GLU GLU A . n A 1 218 ARG 218 545 545 ARG ARG A . n A 1 219 LEU 219 546 546 LEU LEU A . n A 1 220 ILE 220 547 547 ILE ILE A . n A 1 221 TYR 221 548 548 TYR TYR A . n A 1 222 PHE 222 549 549 PHE PHE A . n A 1 223 TYR 223 550 550 TYR TYR A . n A 1 224 VAL 224 551 551 VAL VAL A . n A 1 225 THR 225 552 552 THR THR A . n A 1 226 THR 226 553 553 THR THR A . n A 1 227 HIS 227 554 554 HIS HIS A . n A 1 228 HIS 228 555 ? ? ? A . n A 1 229 HIS 229 556 ? ? ? A . n A 1 230 HIS 230 557 ? ? ? A . n A 1 231 HIS 231 558 ? ? ? A . n A 1 232 HIS 232 559 ? ? ? 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 NAG 1 601 601 NAG NAG A . C 2 NAG 1 602 701 NAG NAG A . D 3 HOH 1 701 2002 HOH HOH A . D 3 HOH 2 702 2004 HOH HOH A . D 3 HOH 3 703 2015 HOH HOH A . D 3 HOH 4 704 2009 HOH HOH A . D 3 HOH 5 705 2018 HOH HOH A . D 3 HOH 6 706 2003 HOH HOH A . D 3 HOH 7 707 2019 HOH HOH A . D 3 HOH 8 708 2001 HOH HOH A . D 3 HOH 9 709 2008 HOH HOH A . D 3 HOH 10 710 2014 HOH HOH A . D 3 HOH 11 711 2007 HOH HOH A . D 3 HOH 12 712 2005 HOH HOH A . D 3 HOH 13 713 2006 HOH HOH A . D 3 HOH 14 714 2012 HOH HOH A . D 3 HOH 15 715 2021 HOH HOH A . D 3 HOH 16 716 2010 HOH HOH A . D 3 HOH 17 717 2020 HOH HOH A . D 3 HOH 18 718 2011 HOH HOH A . D 3 HOH 19 719 2013 HOH HOH A . D 3 HOH 20 720 2017 HOH HOH A . D 3 HOH 21 721 2016 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 ASN 84 A ASN 411 ? ASN 'GLYCOSYLATION SITE' 2 A ASN 188 A ASN 515 ? ASN 'GLYCOSYLATION SITE' # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B,C,D 2 1 A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 712 ? D HOH . 2 1 A HOH 721 ? D HOH . # 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 2013-07-31 2 'Structure model' 1 1 2013-08-21 3 'Structure model' 2 0 2018-04-11 4 'Structure model' 2 1 2019-01-30 5 'Structure model' 2 2 2019-04-24 6 'Structure model' 2 3 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 6 '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' 'Database references' 2 3 'Structure model' 'Atomic model' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Experimental preparation' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Source and taxonomy' 9 6 'Structure model' 'Data collection' 10 6 'Structure model' 'Derived calculations' 11 6 'Structure model' Other 12 6 '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 3 'Structure model' atom_site 2 3 'Structure model' pdbx_nonpoly_scheme 3 3 'Structure model' pdbx_struct_sheet_hbond 4 3 'Structure model' pdbx_struct_special_symmetry 5 3 'Structure model' struct_conf 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_sheet 8 3 'Structure model' struct_sheet_order 9 3 'Structure model' struct_sheet_range 10 3 'Structure model' struct_site 11 4 'Structure model' database_PDB_rev 12 4 'Structure model' database_PDB_rev_record 13 4 'Structure model' exptl_crystal_grow 14 4 'Structure model' struct_biol 15 5 'Structure model' entity_src_gen 16 6 'Structure model' chem_comp 17 6 'Structure model' entity 18 6 'Structure model' pdbx_chem_comp_identifier 19 6 'Structure model' pdbx_database_status 20 6 'Structure model' pdbx_entity_nonpoly 21 6 'Structure model' struct_conn 22 6 'Structure model' struct_site 23 6 '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 3 'Structure model' '_atom_site.B_iso_or_equiv' 2 3 'Structure model' '_atom_site.Cartn_x' 3 3 'Structure model' '_atom_site.Cartn_y' 4 3 'Structure model' '_atom_site.Cartn_z' 5 3 'Structure model' '_atom_site.auth_seq_id' 6 3 'Structure model' '_atom_site.occupancy' 7 3 'Structure model' '_pdbx_nonpoly_scheme.auth_seq_num' 8 3 'Structure model' '_pdbx_nonpoly_scheme.pdb_seq_num' 9 3 'Structure model' '_pdbx_struct_special_symmetry.auth_seq_id' 10 3 'Structure model' '_struct_conf.pdbx_PDB_helix_id' 11 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 3 'Structure model' '_struct_site.details' 14 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 15 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 16 3 'Structure model' '_struct_site.pdbx_auth_seq_id' 17 4 'Structure model' '_exptl_crystal_grow.method' 18 4 'Structure model' '_exptl_crystal_grow.temp' 19 5 'Structure model' '_entity_src_gen.pdbx_host_org_cell_line' 20 6 'Structure model' '_chem_comp.name' 21 6 'Structure model' '_chem_comp.type' 22 6 'Structure model' '_entity.pdbx_description' 23 6 'Structure model' '_pdbx_database_status.status_code_sf' 24 6 'Structure model' '_pdbx_entity_nonpoly.name' 25 6 'Structure model' '_struct_conn.pdbx_role' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language PHENIX refinement '(PHENIX.REFINE)' ? 1 ? ? ? ? XDS 'data reduction' . ? 2 ? ? ? ? XDS 'data scaling' . ? 3 ? ? ? ? autoSHARP phasing . ? 4 ? ? ? ? # _pdbx_entry_details.entry_id 4BSJ _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;N-ACETYL GLUCOSAMINE (NAG): THE NAG MOIETIES ARE COVALENTLY LINKED TO ASN411 AND ASN515. ; _pdbx_entry_details.sequence_details ;ASP 328 AND HIS329 ARE A CLONING ARTEFACT AND HIS554 IS PART OF THE HIS-TAG. RESIDUES 470-483 WERE OMITTED FROM THE MODEL DUE TO LACK OF ELECTRON DENSITY. ; _pdbx_entry_details.has_ligand_of_interest ? # 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 LYS A 339 ? ? -135.39 -56.80 2 1 HIS A 438 ? ? 71.59 -12.30 3 1 ASN A 538 ? ? -125.62 -167.60 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ASP 328 ? CG ? A ASP 1 CG 2 1 Y 1 A ASP 328 ? OD1 ? A ASP 1 OD1 3 1 Y 1 A ASP 328 ? OD2 ? A ASP 1 OD2 4 1 Y 1 A HIS 329 ? CG ? A HIS 2 CG 5 1 Y 1 A HIS 329 ? ND1 ? A HIS 2 ND1 6 1 Y 1 A HIS 329 ? CD2 ? A HIS 2 CD2 7 1 Y 1 A HIS 329 ? CE1 ? A HIS 2 CE1 8 1 Y 1 A HIS 329 ? NE2 ? A HIS 2 NE2 9 1 Y 1 A PHE 469 ? CG ? A PHE 142 CG 10 1 Y 1 A PHE 469 ? CD1 ? A PHE 142 CD1 11 1 Y 1 A PHE 469 ? CD2 ? A PHE 142 CD2 12 1 Y 1 A PHE 469 ? CE1 ? A PHE 142 CE1 13 1 Y 1 A PHE 469 ? CE2 ? A PHE 142 CE2 14 1 Y 1 A PHE 469 ? CZ ? A PHE 142 CZ 15 1 Y 1 A GLN 485 ? CG ? A GLN 158 CG 16 1 Y 1 A GLN 485 ? CD ? A GLN 158 CD 17 1 Y 1 A GLN 485 ? OE1 ? A GLN 158 OE1 18 1 Y 1 A GLN 485 ? NE2 ? A GLN 158 NE2 19 1 Y 1 A ARG 487 ? CG ? A ARG 160 CG 20 1 Y 1 A ARG 487 ? CD ? A ARG 160 CD 21 1 Y 1 A ARG 487 ? NE ? A ARG 160 NE 22 1 Y 1 A ARG 487 ? CZ ? A ARG 160 CZ 23 1 Y 1 A ARG 487 ? NH1 ? A ARG 160 NH1 24 1 Y 1 A ARG 487 ? NH2 ? A ARG 160 NH2 # 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 ALA 470 ? A ALA 143 2 1 Y 1 A GLN 471 ? A GLN 144 3 1 Y 1 A ARG 472 ? A ARG 145 4 1 Y 1 A SER 473 ? A SER 146 5 1 Y 1 A LEU 474 ? A LEU 147 6 1 Y 1 A ARG 475 ? A ARG 148 7 1 Y 1 A ARG 476 ? A ARG 149 8 1 Y 1 A ARG 477 ? A ARG 150 9 1 Y 1 A GLN 478 ? A GLN 151 10 1 Y 1 A GLN 479 ? A GLN 152 11 1 Y 1 A GLN 480 ? A GLN 153 12 1 Y 1 A ASP 481 ? A ASP 154 13 1 Y 1 A LEU 482 ? A LEU 155 14 1 Y 1 A MET 483 ? A MET 156 15 1 Y 1 A HIS 555 ? A HIS 228 16 1 Y 1 A HIS 556 ? A HIS 229 17 1 Y 1 A HIS 557 ? A HIS 230 18 1 Y 1 A HIS 558 ? A HIS 231 19 1 Y 1 A HIS 559 ? A HIS 232 # 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 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_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 3 water HOH #