data_4RN5 # _entry.id 4RN5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code RCSB RCSB087552 PDB 4RN5 WWPDB D_1000087552 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4RN8 . unspecified PDB 4RN9 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RN5 _pdbx_database_status.recvd_initial_deposition_date 2014-10-23 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Allerston, C.K.' 1 'Yelland, T.S.' 2 'Jarvis, A.' 3 'Jenkins, K.' 4 'Winfield, N.' 5 'Cheng, L.' 6 'Jia, H.' 7 'Zachary, I.' 8 'Selwood, D.L.' 9 'Djordjevic, S.' 10 # _citation.id primary _citation.title 'Conserved water molecules in a ligand-binding site of neuropilin-1' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Allerston, C.K.' 1 primary 'Yelland, T.S.' 2 primary 'Jarvis, A.' 3 primary 'Jenkins, K.' 4 primary 'Winfield, N.' 5 primary 'Cheng, L.' 6 primary 'Jia, H.' 7 primary 'Zachary, I.' 8 primary 'Selwood, D.L.' 9 primary 'Djordjevic, S.' 10 # _cell.entry_id 4RN5 _cell.length_a 62.839 _cell.length_b 62.839 _cell.length_c 87.918 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4RN5 _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _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 Neuropilin-1 17917.291 1 ? ? 'B1 domain (UNP residues 273-427)' ? 2 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 water nat water 18.015 159 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Vascular endothelial cell growth factor 165 receptor' # _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 ;GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT ; _entity_poly.pdbx_seq_one_letter_code_can ;GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT ; _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 GLY n 1 2 HIS n 1 3 MET n 1 4 PHE n 1 5 LYS n 1 6 CYS n 1 7 MET n 1 8 GLU n 1 9 ALA n 1 10 LEU n 1 11 GLY n 1 12 MET n 1 13 GLU n 1 14 SER n 1 15 GLY n 1 16 GLU n 1 17 ILE n 1 18 HIS n 1 19 SER n 1 20 ASP n 1 21 GLN n 1 22 ILE n 1 23 THR n 1 24 ALA n 1 25 SER n 1 26 SER n 1 27 GLN n 1 28 TYR n 1 29 SER n 1 30 THR n 1 31 ASN n 1 32 TRP n 1 33 SER n 1 34 ALA n 1 35 GLU n 1 36 ARG n 1 37 SER n 1 38 ARG n 1 39 LEU n 1 40 ASN n 1 41 TYR n 1 42 PRO n 1 43 GLU n 1 44 ASN n 1 45 GLY n 1 46 TRP n 1 47 THR n 1 48 PRO n 1 49 GLY n 1 50 GLU n 1 51 ASP n 1 52 SER n 1 53 TYR n 1 54 ARG n 1 55 GLU n 1 56 TRP n 1 57 ILE n 1 58 GLN n 1 59 VAL n 1 60 ASP n 1 61 LEU n 1 62 GLY n 1 63 LEU n 1 64 LEU n 1 65 ARG n 1 66 PHE n 1 67 VAL n 1 68 THR n 1 69 ALA n 1 70 VAL n 1 71 GLY n 1 72 THR n 1 73 GLN n 1 74 GLY n 1 75 ALA n 1 76 ILE n 1 77 SER n 1 78 LYS n 1 79 GLU n 1 80 THR n 1 81 LYS n 1 82 LYS n 1 83 LYS n 1 84 TYR n 1 85 TYR n 1 86 VAL n 1 87 LYS n 1 88 THR n 1 89 TYR n 1 90 LYS n 1 91 ILE n 1 92 ASP n 1 93 VAL n 1 94 SER n 1 95 SER n 1 96 ASN n 1 97 GLY n 1 98 GLU n 1 99 ASP n 1 100 TRP n 1 101 ILE n 1 102 THR n 1 103 ILE n 1 104 LYS n 1 105 GLU n 1 106 GLY n 1 107 ASN n 1 108 LYS n 1 109 PRO n 1 110 VAL n 1 111 LEU n 1 112 PHE n 1 113 GLN n 1 114 GLY n 1 115 ASN n 1 116 THR n 1 117 ASN n 1 118 PRO n 1 119 THR n 1 120 ASP n 1 121 VAL n 1 122 VAL n 1 123 VAL n 1 124 ALA n 1 125 VAL n 1 126 PHE n 1 127 PRO n 1 128 LYS n 1 129 PRO n 1 130 LEU n 1 131 ILE n 1 132 THR n 1 133 ARG n 1 134 PHE n 1 135 VAL n 1 136 ARG n 1 137 ILE n 1 138 LYS n 1 139 PRO n 1 140 ALA n 1 141 THR n 1 142 TRP n 1 143 GLU n 1 144 THR n 1 145 GLY n 1 146 ILE n 1 147 SER n 1 148 MET n 1 149 ARG n 1 150 PHE n 1 151 GLU n 1 152 VAL n 1 153 TYR n 1 154 GLY n 1 155 CYS n 1 156 LYS n 1 157 ILE n 1 158 THR n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'NRP1, NRP, VEGF165R' _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 ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NRP1_HUMAN _struct_ref.pdbx_db_accession O14786 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;FKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKK YYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT ; _struct_ref.pdbx_align_begin 273 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RN5 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 158 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O14786 _struct_ref_seq.db_align_beg 273 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 427 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 273 _struct_ref_seq.pdbx_auth_seq_align_end 427 # 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 4RN5 GLY A 1 ? UNP O14786 ? ? 'EXPRESSION TAG' 270 1 1 4RN5 HIS A 2 ? UNP O14786 ? ? 'EXPRESSION TAG' 271 2 1 4RN5 MET A 3 ? UNP O14786 ? ? 'EXPRESSION TAG' 272 3 # 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 ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 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 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.entry_id 4RN5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.42 _exptl_crystal.density_percent_sol 49.22 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '100mM MES, 200mM Zinc Acetate, 10% PEG 8000, pH 6.0, VAPOR DIFFUSION, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2009-12-01 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 4RN5 _reflns.observed_criterion_sigma_I 1.34 _reflns.observed_criterion_sigma_F 1.34 _reflns.d_resolution_low 21.540 _reflns.d_resolution_high 1.73 _reflns.number_obs 16198 _reflns.number_all 16198 _reflns.percent_possible_obs 84.87 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.73 _reflns_shell.d_res_low 1.84 _reflns_shell.percent_possible_all 31 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4RN5 _refine.ls_number_reflns_obs 16198 _refine.ls_number_reflns_all 16198 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 21.540 _refine.ls_d_res_high 1.73 _refine.ls_percent_reflns_obs 84.87 _refine.ls_R_factor_obs 0.1776 _refine.ls_R_factor_R_work 0.1763 _refine.ls_R_factor_R_free 0.2008 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.99 _refine.ls_number_reflns_R_free 808 _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 ? _refine.aniso_B[1][1] -0.1475 _refine.aniso_B[2][2] -0.1475 _refine.aniso_B[3][3] 0.2949 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.359 _refine.solvent_model_param_bsol 40.416 _refine.pdbx_solvent_vdw_probe_radii 0.90 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.60 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.18 _refine.pdbx_overall_phase_error 20.42 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_R_factor_all ? _refine.pdbx_TLS_residual_ADP_flag ? _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 1261 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 159 _refine_hist.number_atoms_total 1432 _refine_hist.d_res_high 1.73 _refine_hist.d_res_low 21.540 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.013 ? ? 1301 ? 'X-RAY DIFFRACTION' f_angle_d 1.384 ? ? 1759 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 14.640 ? ? 476 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.102 ? ? 189 ? 'X-RAY DIFFRACTION' f_plane_restr 0.007 ? ? 223 ? 'X-RAY DIFFRACTION' # loop_ _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 _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 1.73 1.8360 901 0.2993 31.00 0.3872 . . 46 . . . . 'X-RAY DIFFRACTION' . 1.8360 1.9776 2347 0.1897 79.00 0.2540 . . 122 . . . . 'X-RAY DIFFRACTION' . 1.9776 2.1765 2887 0.1666 98.00 0.2116 . . 171 . . . . 'X-RAY DIFFRACTION' . 2.1765 2.4910 2998 0.1687 100.00 0.2178 . . 149 . . . . 'X-RAY DIFFRACTION' . 2.4910 3.1368 3039 0.1774 100.00 0.1884 . . 175 . . . . 'X-RAY DIFFRACTION' . 3.1368 21.5414 3218 0.1734 100.00 0.1781 . . 145 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 4RN5 _struct.title 'B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site' _struct.pdbx_descriptor Neuropilin-1 _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RN5 _struct_keywords.pdbx_keywords 'PROTEIN BINDING' _struct_keywords.text 'VEGF binding, PROTEIN BINDING' # 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 4 ? F N N 5 ? # _struct_biol.id 1 _struct_biol.details ? # 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 HIS A 18 ? ASP A 20 ? HIS A 287 ASP A 289 5 ? 3 HELX_P HELX_P2 2 SER A 29 ? ARG A 38 ? SER A 298 ARG A 307 5 ? 10 # _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 disulf1 disulf ? ? A CYS 6 SG ? ? ? 1_555 A CYS 155 SG ? ? A CYS 275 A CYS 424 1_555 ? ? ? ? ? ? ? 2.028 ? metalc1 metalc ? ? A HIS 18 NE2 ? ? ? 1_555 C ZN . ZN ? ? A HIS 287 A ZN 502 1_555 ? ? ? ? ? ? ? 2.097 ? metalc2 metalc ? ? C ZN . ZN ? ? ? 1_555 F HOH . O ? ? A ZN 502 A HOH 685 1_555 ? ? ? ? ? ? ? 2.254 ? metalc3 metalc ? ? D ZN . ZN ? ? ? 1_555 F HOH . O ? ? A ZN 503 A HOH 755 1_555 ? ? ? ? ? ? ? 2.417 ? metalc4 metalc ? ? D ZN . ZN ? ? ? 1_555 F HOH . O ? ? A ZN 503 A HOH 756 1_555 ? ? ? ? ? ? ? 2.444 ? metalc5 metalc ? ? A ASP 20 OD2 ? ? ? 1_555 D ZN . ZN ? ? A ASP 289 A ZN 503 1_555 ? ? ? ? ? ? ? 2.570 ? metalc6 metalc ? ? D ZN . ZN ? ? ? 1_555 F HOH . O ? ? A ZN 503 A HOH 757 1_555 ? ? ? ? ? ? ? 2.597 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? metalc ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 5 ? C ? 3 ? D ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel D 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLU A 8 ? ALA A 9 ? GLU A 277 ALA A 278 A 2 ARG A 149 ? CYS A 155 ? ARG A 418 CYS A 424 A 3 ILE A 57 ? GLN A 73 ? ILE A 326 GLN A 342 A 4 VAL A 122 ? GLU A 143 ? VAL A 391 GLU A 412 A 5 LYS A 83 ? SER A 94 ? LYS A 352 SER A 363 A 6 TRP A 100 ? THR A 102 ? TRP A 369 THR A 371 B 1 PHE A 112 ? GLN A 113 ? PHE A 381 GLN A 382 B 2 LYS A 83 ? SER A 94 ? LYS A 352 SER A 363 B 3 VAL A 122 ? GLU A 143 ? VAL A 391 GLU A 412 B 4 ILE A 57 ? GLN A 73 ? ILE A 326 GLN A 342 B 5 ILE A 22 ? ALA A 24 ? ILE A 291 ALA A 293 C 1 ALA A 75 ? ILE A 76 ? ALA A 344 ILE A 345 C 2 LYS A 83 ? SER A 94 ? LYS A 352 SER A 363 C 3 TRP A 100 ? THR A 102 ? TRP A 369 THR A 371 D 1 LYS A 104 ? GLU A 105 ? LYS A 373 GLU A 374 D 2 LYS A 108 ? PRO A 109 ? LYS A 377 PRO A 378 # 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 GLU A 8 ? N GLU A 277 O GLY A 154 ? O GLY A 423 A 2 3 O TYR A 153 ? O TYR A 422 N ALA A 69 ? N ALA A 338 A 3 4 N VAL A 70 ? N VAL A 339 O ALA A 124 ? O ALA A 393 A 4 5 O LYS A 138 ? O LYS A 407 N LYS A 90 ? N LYS A 359 A 5 6 N VAL A 93 ? N VAL A 362 O ILE A 101 ? O ILE A 370 B 1 2 O PHE A 112 ? O PHE A 381 N TYR A 89 ? N TYR A 358 B 2 3 N LYS A 90 ? N LYS A 359 O LYS A 138 ? O LYS A 407 B 3 4 O ALA A 124 ? O ALA A 393 N VAL A 70 ? N VAL A 339 B 4 5 O GLN A 58 ? O GLN A 327 N THR A 23 ? N THR A 292 C 1 2 N ALA A 75 ? N ALA A 344 O TYR A 84 ? O TYR A 353 C 2 3 N VAL A 93 ? N VAL A 362 O ILE A 101 ? O ILE A 370 D 1 2 N GLU A 105 ? N GLU A 374 O LYS A 108 ? O LYS A 377 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE ACT A 501' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 502' AC3 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE ZN A 503' AC4 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE GOL A 504' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 TRP A 32 ? TRP A 301 . ? 1_555 ? 2 AC1 6 SER A 77 ? SER A 346 . ? 1_555 ? 3 AC1 6 THR A 80 ? THR A 349 . ? 1_555 ? 4 AC1 6 TYR A 84 ? TYR A 353 . ? 1_555 ? 5 AC1 6 ARG A 133 ? ARG A 402 . ? 6_454 ? 6 AC1 6 HOH F . ? HOH A 643 . ? 6_454 ? 7 AC2 4 GLY A 1 ? GLY A 270 . ? 4_454 ? 8 AC2 4 HIS A 18 ? HIS A 287 . ? 1_555 ? 9 AC2 4 GLU A 50 ? GLU A 319 . ? 6_554 ? 10 AC2 4 HOH F . ? HOH A 685 . ? 1_555 ? 11 AC3 6 ASP A 20 ? ASP A 289 . ? 1_555 ? 12 AC3 6 ASP A 51 ? ASP A 320 . ? 6_554 ? 13 AC3 6 HOH F . ? HOH A 755 . ? 1_555 ? 14 AC3 6 HOH F . ? HOH A 756 . ? 1_555 ? 15 AC3 6 HOH F . ? HOH A 757 . ? 1_555 ? 16 AC3 6 HOH F . ? HOH A 759 . ? 1_555 ? 17 AC4 7 LEU A 10 ? LEU A 279 . ? 1_555 ? 18 AC4 7 GLU A 16 ? GLU A 285 . ? 1_555 ? 19 AC4 7 GLN A 21 ? GLN A 290 . ? 1_555 ? 20 AC4 7 LEU A 61 ? LEU A 330 . ? 1_555 ? 21 AC4 7 ARG A 65 ? ARG A 334 . ? 1_555 ? 22 AC4 7 HOH F . ? HOH A 679 . ? 1_555 ? 23 AC4 7 HOH F . ? HOH A 713 . ? 1_555 ? # _database_PDB_matrix.entry_id 4RN5 _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 4RN5 _atom_sites.fract_transf_matrix[1][1] 0.015914 _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] 0.015914 _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] 0.011374 _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 ZN # 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 GLY 1 270 270 GLY GLY A . n A 1 2 HIS 2 271 271 HIS HIS A . n A 1 3 MET 3 272 272 MET MET A . n A 1 4 PHE 4 273 273 PHE PHE A . n A 1 5 LYS 5 274 274 LYS LYS A . n A 1 6 CYS 6 275 275 CYS CYS A . n A 1 7 MET 7 276 276 MET MET A . n A 1 8 GLU 8 277 277 GLU GLU A . n A 1 9 ALA 9 278 278 ALA ALA A . n A 1 10 LEU 10 279 279 LEU LEU A . n A 1 11 GLY 11 280 280 GLY GLY A . n A 1 12 MET 12 281 281 MET MET A . n A 1 13 GLU 13 282 282 GLU GLU A . n A 1 14 SER 14 283 283 SER SER A . n A 1 15 GLY 15 284 284 GLY GLY A . n A 1 16 GLU 16 285 285 GLU GLU A . n A 1 17 ILE 17 286 286 ILE ILE A . n A 1 18 HIS 18 287 287 HIS HIS A . n A 1 19 SER 19 288 288 SER SER A . n A 1 20 ASP 20 289 289 ASP ASP A . n A 1 21 GLN 21 290 290 GLN GLN A . n A 1 22 ILE 22 291 291 ILE ILE A . n A 1 23 THR 23 292 292 THR THR A . n A 1 24 ALA 24 293 293 ALA ALA A . n A 1 25 SER 25 294 294 SER SER A . n A 1 26 SER 26 295 295 SER SER A . n A 1 27 GLN 27 296 296 GLN GLN A . n A 1 28 TYR 28 297 297 TYR TYR A . n A 1 29 SER 29 298 298 SER SER A . n A 1 30 THR 30 299 299 THR THR A . n A 1 31 ASN 31 300 300 ASN ASN A . n A 1 32 TRP 32 301 301 TRP TRP A . n A 1 33 SER 33 302 302 SER SER A . n A 1 34 ALA 34 303 303 ALA ALA A . n A 1 35 GLU 35 304 304 GLU GLU A . n A 1 36 ARG 36 305 305 ARG ARG A . n A 1 37 SER 37 306 306 SER SER A . n A 1 38 ARG 38 307 307 ARG ARG A . n A 1 39 LEU 39 308 308 LEU LEU A . n A 1 40 ASN 40 309 309 ASN ASN A . n A 1 41 TYR 41 310 310 TYR TYR A . n A 1 42 PRO 42 311 311 PRO PRO A . n A 1 43 GLU 43 312 312 GLU GLU A . n A 1 44 ASN 44 313 313 ASN ASN A . n A 1 45 GLY 45 314 314 GLY GLY A . n A 1 46 TRP 46 315 315 TRP TRP A . n A 1 47 THR 47 316 316 THR THR A . n A 1 48 PRO 48 317 317 PRO PRO A . n A 1 49 GLY 49 318 318 GLY GLY A . n A 1 50 GLU 50 319 319 GLU GLU A . n A 1 51 ASP 51 320 320 ASP ASP A . n A 1 52 SER 52 321 321 SER SER A . n A 1 53 TYR 53 322 322 TYR TYR A . n A 1 54 ARG 54 323 323 ARG ARG A . n A 1 55 GLU 55 324 324 GLU GLU A . n A 1 56 TRP 56 325 325 TRP TRP A . n A 1 57 ILE 57 326 326 ILE ILE A . n A 1 58 GLN 58 327 327 GLN GLN A . n A 1 59 VAL 59 328 328 VAL VAL A . n A 1 60 ASP 60 329 329 ASP ASP A . n A 1 61 LEU 61 330 330 LEU LEU A . n A 1 62 GLY 62 331 331 GLY GLY A . n A 1 63 LEU 63 332 332 LEU LEU A . n A 1 64 LEU 64 333 333 LEU LEU A . n A 1 65 ARG 65 334 334 ARG ARG A . n A 1 66 PHE 66 335 335 PHE PHE A . n A 1 67 VAL 67 336 336 VAL VAL A . n A 1 68 THR 68 337 337 THR THR A . n A 1 69 ALA 69 338 338 ALA ALA A . n A 1 70 VAL 70 339 339 VAL VAL A . n A 1 71 GLY 71 340 340 GLY GLY A . n A 1 72 THR 72 341 341 THR THR A . n A 1 73 GLN 73 342 342 GLN GLN A . n A 1 74 GLY 74 343 343 GLY GLY A . n A 1 75 ALA 75 344 344 ALA ALA A . n A 1 76 ILE 76 345 345 ILE ILE A . n A 1 77 SER 77 346 346 SER SER A . n A 1 78 LYS 78 347 347 LYS LYS A . n A 1 79 GLU 79 348 348 GLU GLU A . n A 1 80 THR 80 349 349 THR THR A . n A 1 81 LYS 81 350 350 LYS LYS A . n A 1 82 LYS 82 351 351 LYS LYS A . n A 1 83 LYS 83 352 352 LYS LYS A . n A 1 84 TYR 84 353 353 TYR TYR A . n A 1 85 TYR 85 354 354 TYR TYR A . n A 1 86 VAL 86 355 355 VAL VAL A . n A 1 87 LYS 87 356 356 LYS LYS A . n A 1 88 THR 88 357 357 THR THR A . n A 1 89 TYR 89 358 358 TYR TYR A . n A 1 90 LYS 90 359 359 LYS LYS A . n A 1 91 ILE 91 360 360 ILE ILE A . n A 1 92 ASP 92 361 361 ASP ASP A . n A 1 93 VAL 93 362 362 VAL VAL A . n A 1 94 SER 94 363 363 SER SER A . n A 1 95 SER 95 364 364 SER SER A . n A 1 96 ASN 96 365 365 ASN ASN A . n A 1 97 GLY 97 366 366 GLY GLY A . n A 1 98 GLU 98 367 367 GLU GLU A . n A 1 99 ASP 99 368 368 ASP ASP A . n A 1 100 TRP 100 369 369 TRP TRP A . n A 1 101 ILE 101 370 370 ILE ILE A . n A 1 102 THR 102 371 371 THR THR A . n A 1 103 ILE 103 372 372 ILE ILE A . n A 1 104 LYS 104 373 373 LYS LYS A . n A 1 105 GLU 105 374 374 GLU GLU A . n A 1 106 GLY 106 375 375 GLY GLY A . n A 1 107 ASN 107 376 376 ASN ASN A . n A 1 108 LYS 108 377 377 LYS LYS A . n A 1 109 PRO 109 378 378 PRO PRO A . n A 1 110 VAL 110 379 379 VAL VAL A . n A 1 111 LEU 111 380 380 LEU LEU A . n A 1 112 PHE 112 381 381 PHE PHE A . n A 1 113 GLN 113 382 382 GLN GLN A . n A 1 114 GLY 114 383 383 GLY GLY A . n A 1 115 ASN 115 384 384 ASN ASN A . n A 1 116 THR 116 385 385 THR THR A . n A 1 117 ASN 117 386 386 ASN ASN A . n A 1 118 PRO 118 387 387 PRO PRO A . n A 1 119 THR 119 388 388 THR THR A . n A 1 120 ASP 120 389 389 ASP ASP A . n A 1 121 VAL 121 390 390 VAL VAL A . n A 1 122 VAL 122 391 391 VAL VAL A . n A 1 123 VAL 123 392 392 VAL VAL A . n A 1 124 ALA 124 393 393 ALA ALA A . n A 1 125 VAL 125 394 394 VAL VAL A . n A 1 126 PHE 126 395 395 PHE PHE A . n A 1 127 PRO 127 396 396 PRO PRO A . n A 1 128 LYS 128 397 397 LYS LYS A . n A 1 129 PRO 129 398 398 PRO PRO A . n A 1 130 LEU 130 399 399 LEU LEU A . n A 1 131 ILE 131 400 400 ILE ILE A . n A 1 132 THR 132 401 401 THR THR A . n A 1 133 ARG 133 402 402 ARG ARG A . n A 1 134 PHE 134 403 403 PHE PHE A . n A 1 135 VAL 135 404 404 VAL VAL A . n A 1 136 ARG 136 405 405 ARG ARG A . n A 1 137 ILE 137 406 406 ILE ILE A . n A 1 138 LYS 138 407 407 LYS LYS A . n A 1 139 PRO 139 408 408 PRO PRO A . n A 1 140 ALA 140 409 409 ALA ALA A . n A 1 141 THR 141 410 410 THR THR A . n A 1 142 TRP 142 411 411 TRP TRP A . n A 1 143 GLU 143 412 412 GLU GLU A . n A 1 144 THR 144 413 413 THR THR A . n A 1 145 GLY 145 414 414 GLY GLY A . n A 1 146 ILE 146 415 415 ILE ILE A . n A 1 147 SER 147 416 416 SER SER A . n A 1 148 MET 148 417 417 MET MET A . n A 1 149 ARG 149 418 418 ARG ARG A . n A 1 150 PHE 150 419 419 PHE PHE A . n A 1 151 GLU 151 420 420 GLU GLU A . n A 1 152 VAL 152 421 421 VAL VAL A . n A 1 153 TYR 153 422 422 TYR TYR A . n A 1 154 GLY 154 423 423 GLY GLY A . n A 1 155 CYS 155 424 424 CYS CYS A . n A 1 156 LYS 156 425 425 LYS LYS A . n A 1 157 ILE 157 426 426 ILE ILE A . n A 1 158 THR 158 427 427 THR THR 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 ACT 1 501 1 ACT ACT A . C 3 ZN 1 502 1 ZN ZN A . D 3 ZN 1 503 2 ZN ZN A . E 4 GOL 1 504 1 GOL GOL A . F 5 HOH 1 601 1 HOH HOH A . F 5 HOH 2 602 2 HOH HOH A . F 5 HOH 3 603 3 HOH HOH A . F 5 HOH 4 604 4 HOH HOH A . F 5 HOH 5 605 5 HOH HOH A . F 5 HOH 6 606 6 HOH HOH A . F 5 HOH 7 607 7 HOH HOH A . F 5 HOH 8 608 8 HOH HOH A . F 5 HOH 9 609 9 HOH HOH A . F 5 HOH 10 610 10 HOH HOH A . F 5 HOH 11 611 11 HOH HOH A . F 5 HOH 12 612 12 HOH HOH A . F 5 HOH 13 613 13 HOH HOH A . F 5 HOH 14 614 14 HOH HOH A . F 5 HOH 15 615 15 HOH HOH A . F 5 HOH 16 616 16 HOH HOH A . F 5 HOH 17 617 17 HOH HOH A . F 5 HOH 18 618 18 HOH HOH A . F 5 HOH 19 619 19 HOH HOH A . F 5 HOH 20 620 20 HOH HOH A . F 5 HOH 21 621 21 HOH HOH A . F 5 HOH 22 622 22 HOH HOH A . F 5 HOH 23 623 23 HOH HOH A . F 5 HOH 24 624 24 HOH HOH A . F 5 HOH 25 625 25 HOH HOH A . F 5 HOH 26 626 26 HOH HOH A . F 5 HOH 27 627 27 HOH HOH A . F 5 HOH 28 628 28 HOH HOH A . F 5 HOH 29 629 29 HOH HOH A . F 5 HOH 30 630 30 HOH HOH A . F 5 HOH 31 631 31 HOH HOH A . F 5 HOH 32 632 32 HOH HOH A . F 5 HOH 33 633 33 HOH HOH A . F 5 HOH 34 634 34 HOH HOH A . F 5 HOH 35 635 35 HOH HOH A . F 5 HOH 36 636 36 HOH HOH A . F 5 HOH 37 637 37 HOH HOH A . F 5 HOH 38 638 38 HOH HOH A . F 5 HOH 39 639 39 HOH HOH A . F 5 HOH 40 640 40 HOH HOH A . F 5 HOH 41 641 41 HOH HOH A . F 5 HOH 42 642 42 HOH HOH A . F 5 HOH 43 643 43 HOH HOH A . F 5 HOH 44 644 44 HOH HOH A . F 5 HOH 45 645 45 HOH HOH A . F 5 HOH 46 646 46 HOH HOH A . F 5 HOH 47 647 47 HOH HOH A . F 5 HOH 48 648 48 HOH HOH A . F 5 HOH 49 649 49 HOH HOH A . F 5 HOH 50 650 50 HOH HOH A . F 5 HOH 51 651 51 HOH HOH A . F 5 HOH 52 652 52 HOH HOH A . F 5 HOH 53 653 53 HOH HOH A . F 5 HOH 54 654 54 HOH HOH A . F 5 HOH 55 655 55 HOH HOH A . F 5 HOH 56 656 56 HOH HOH A . F 5 HOH 57 657 57 HOH HOH A . F 5 HOH 58 658 58 HOH HOH A . F 5 HOH 59 659 59 HOH HOH A . F 5 HOH 60 660 60 HOH HOH A . F 5 HOH 61 661 61 HOH HOH A . F 5 HOH 62 662 62 HOH HOH A . F 5 HOH 63 663 63 HOH HOH A . F 5 HOH 64 664 64 HOH HOH A . F 5 HOH 65 665 65 HOH HOH A . F 5 HOH 66 666 66 HOH HOH A . F 5 HOH 67 667 67 HOH HOH A . F 5 HOH 68 668 68 HOH HOH A . F 5 HOH 69 669 69 HOH HOH A . F 5 HOH 70 670 70 HOH HOH A . F 5 HOH 71 671 71 HOH HOH A . F 5 HOH 72 672 72 HOH HOH A . F 5 HOH 73 673 73 HOH HOH A . F 5 HOH 74 674 74 HOH HOH A . F 5 HOH 75 675 75 HOH HOH A . F 5 HOH 76 676 76 HOH HOH A . F 5 HOH 77 677 77 HOH HOH A . F 5 HOH 78 678 78 HOH HOH A . F 5 HOH 79 679 79 HOH HOH A . F 5 HOH 80 680 80 HOH HOH A . F 5 HOH 81 681 81 HOH HOH A . F 5 HOH 82 682 82 HOH HOH A . F 5 HOH 83 683 83 HOH HOH A . F 5 HOH 84 684 84 HOH HOH A . F 5 HOH 85 685 85 HOH HOH A . F 5 HOH 86 686 86 HOH HOH A . F 5 HOH 87 687 87 HOH HOH A . F 5 HOH 88 688 88 HOH HOH A . F 5 HOH 89 689 89 HOH HOH A . F 5 HOH 90 690 90 HOH HOH A . F 5 HOH 91 691 91 HOH HOH A . F 5 HOH 92 692 92 HOH HOH A . F 5 HOH 93 693 93 HOH HOH A . F 5 HOH 94 694 94 HOH HOH A . F 5 HOH 95 695 95 HOH HOH A . F 5 HOH 96 696 96 HOH HOH A . F 5 HOH 97 697 97 HOH HOH A . F 5 HOH 98 698 98 HOH HOH A . F 5 HOH 99 699 99 HOH HOH A . F 5 HOH 100 700 100 HOH HOH A . F 5 HOH 101 701 101 HOH HOH A . F 5 HOH 102 702 102 HOH HOH A . F 5 HOH 103 703 103 HOH HOH A . F 5 HOH 104 704 104 HOH HOH A . F 5 HOH 105 705 105 HOH HOH A . F 5 HOH 106 706 106 HOH HOH A . F 5 HOH 107 707 107 HOH HOH A . F 5 HOH 108 708 108 HOH HOH A . F 5 HOH 109 709 109 HOH HOH A . F 5 HOH 110 710 110 HOH HOH A . F 5 HOH 111 711 111 HOH HOH A . F 5 HOH 112 712 112 HOH HOH A . F 5 HOH 113 713 113 HOH HOH A . F 5 HOH 114 714 114 HOH HOH A . F 5 HOH 115 715 115 HOH HOH A . F 5 HOH 116 716 116 HOH HOH A . F 5 HOH 117 717 117 HOH HOH A . F 5 HOH 118 718 118 HOH HOH A . F 5 HOH 119 719 119 HOH HOH A . F 5 HOH 120 720 120 HOH HOH A . F 5 HOH 121 721 122 HOH HOH A . F 5 HOH 122 722 123 HOH HOH A . F 5 HOH 123 723 124 HOH HOH A . F 5 HOH 124 724 125 HOH HOH A . F 5 HOH 125 725 126 HOH HOH A . F 5 HOH 126 726 127 HOH HOH A . F 5 HOH 127 727 128 HOH HOH A . F 5 HOH 128 728 129 HOH HOH A . F 5 HOH 129 729 130 HOH HOH A . F 5 HOH 130 730 131 HOH HOH A . F 5 HOH 131 731 132 HOH HOH A . F 5 HOH 132 732 133 HOH HOH A . F 5 HOH 133 733 134 HOH HOH A . F 5 HOH 134 734 135 HOH HOH A . F 5 HOH 135 735 136 HOH HOH A . F 5 HOH 136 736 137 HOH HOH A . F 5 HOH 137 737 138 HOH HOH A . F 5 HOH 138 738 139 HOH HOH A . F 5 HOH 139 739 140 HOH HOH A . F 5 HOH 140 740 141 HOH HOH A . F 5 HOH 141 741 142 HOH HOH A . F 5 HOH 142 742 143 HOH HOH A . F 5 HOH 143 743 144 HOH HOH A . F 5 HOH 144 744 145 HOH HOH A . F 5 HOH 145 745 146 HOH HOH A . F 5 HOH 146 746 147 HOH HOH A . F 5 HOH 147 747 148 HOH HOH A . F 5 HOH 148 748 149 HOH HOH A . F 5 HOH 149 749 150 HOH HOH A . F 5 HOH 150 750 151 HOH HOH A . F 5 HOH 151 751 152 HOH HOH A . F 5 HOH 152 752 153 HOH HOH A . F 5 HOH 153 753 154 HOH HOH A . F 5 HOH 154 754 155 HOH HOH A . F 5 HOH 155 755 156 HOH HOH A . F 5 HOH 156 756 157 HOH HOH A . F 5 HOH 157 757 158 HOH HOH A . F 5 HOH 158 758 159 HOH HOH A . F 5 HOH 159 759 160 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 NE2 ? A HIS 18 ? A HIS 287 ? 1_555 ZN ? C ZN . ? A ZN 502 ? 1_555 O ? F HOH . ? A HOH 685 ? 1_555 95.4 ? 2 O ? F HOH . ? A HOH 755 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 O ? F HOH . ? A HOH 756 ? 1_555 97.6 ? 3 O ? F HOH . ? A HOH 755 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 OD2 ? A ASP 20 ? A ASP 289 ? 1_555 81.3 ? 4 O ? F HOH . ? A HOH 756 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 OD2 ? A ASP 20 ? A ASP 289 ? 1_555 100.2 ? 5 O ? F HOH . ? A HOH 755 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 O ? F HOH . ? A HOH 757 ? 1_555 143.8 ? 6 O ? F HOH . ? A HOH 756 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 O ? F HOH . ? A HOH 757 ? 1_555 108.7 ? 7 OD2 ? A ASP 20 ? A ASP 289 ? 1_555 ZN ? D ZN . ? A ZN 503 ? 1_555 O ? F HOH . ? A HOH 757 ? 1_555 116.5 ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2015-10-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrystalClear 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7.3_928)' ? 3 d*TREK 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # 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 274 ? ? 56.08 14.29 2 1 SER A 298 ? ? -171.45 -179.13 3 1 ASN A 313 ? ? 59.14 -143.87 4 1 ASN A 376 ? ? 56.67 13.12 5 1 THR A 413 ? ? 76.51 -45.19 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ACETATE ION' ACT 3 'ZINC ION' ZN 4 GLYCEROL GOL 5 water HOH #