data_5DV3 # _model_server_result.job_id KXPaXwu47ERzW5anLg3BgA _model_server_result.datetime_utc '2024-11-14 23:19:00' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5dv3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5DV3 # _exptl.entry_id 5DV3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 348.352 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[2-(benzyloxy)phenyl]-3-nitrobenzamide _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5DV3 _cell.length_a 53.947 _cell.length_b 130.892 _cell.length_c 52.593 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DV3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 95 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 285 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id CAV _struct_conn.ptnr2_label_comp_id B05 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id B05 _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.693 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H16 N2 O4' _chem_comp.formula_weight 348.352 _chem_comp.id B05 _chem_comp.mon_nstd_flag . _chem_comp.name N-[2-(benzyloxy)phenyl]-3-nitrobenzamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag OAB NBA B05 doub 70 n n CAN CAM B05 doub 71 n y CAN CAW B05 sing 72 n y CAM CAV B05 sing 73 n y NBA CAW B05 sing 74 n n NBA OAC B05 sing 75 n n CAW CAP B05 doub 76 n y CAV CAZ B05 doub 77 n y CAE CAF B05 doub 78 n y CAE CAG B05 sing 79 n y CAF CAJ B05 sing 80 n y CAP CAZ B05 sing 81 n y CAZ CAT B05 sing 82 n n CAG CAK B05 doub 83 n y CAJ CAU B05 doub 84 n y CAT OAA B05 doub 85 n n CAT NAR B05 sing 86 n n CAK CAU B05 sing 87 n y CAU CAQ B05 sing 88 n n NAR CAX B05 sing 89 n n CAQ OAS B05 sing 90 n n OAS CAY B05 sing 91 n n CAX CAY B05 doub 92 n y CAX CAL B05 sing 93 n y CAY CAO B05 sing 94 n y CAL CAH B05 doub 95 n y CAO CAI B05 doub 96 n y CAH CAI B05 sing 97 n y CAK H1 B05 sing 98 n n CAJ H2 B05 sing 99 n n CAI H3 B05 sing 100 n n CAV H4 B05 sing 101 n n CAQ H5 B05 sing 102 n n CAQ H6 B05 sing 103 n n CAP H7 B05 sing 104 n n CAO H8 B05 sing 105 n n CAN H9 B05 sing 106 n n CAM H10 B05 sing 107 n n CAL H11 B05 sing 108 n n NAR H12 B05 sing 109 n n CAH H13 B05 sing 110 n n CAF H14 B05 sing 111 n n CAE H15 B05 sing 112 n n CAG H16 B05 sing 113 n n # _atom_sites.entry_id 5DV3 _atom_sites.fract_transf_matrix[1][1] 0.018537 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00764 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.019014 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code C 3 B05 A 1 501 501 B05 B05 . D 4 HOH A 1 601 623 HOH HOH . D 4 HOH A 2 602 605 HOH HOH . D 4 HOH A 3 603 619 HOH HOH . D 4 HOH A 4 604 616 HOH HOH . D 4 HOH A 5 605 602 HOH HOH . D 4 HOH A 6 606 609 HOH HOH . D 4 HOH A 7 607 606 HOH HOH . D 4 HOH A 8 608 621 HOH HOH . D 4 HOH A 9 609 620 HOH HOH . D 4 HOH A 10 610 603 HOH HOH . D 4 HOH A 11 611 625 HOH HOH . D 4 HOH A 12 612 622 HOH HOH . D 4 HOH A 13 613 624 HOH HOH . D 4 HOH A 14 614 613 HOH HOH . D 4 HOH A 15 615 604 HOH HOH . D 4 HOH A 16 616 614 HOH HOH . D 4 HOH A 17 617 611 HOH HOH . D 4 HOH A 18 618 601 HOH HOH . D 4 HOH A 19 619 610 HOH HOH . D 4 HOH A 20 620 615 HOH HOH . D 4 HOH A 21 621 607 HOH HOH . D 4 HOH A 22 622 608 HOH HOH . D 4 HOH A 23 623 612 HOH HOH . D 4 HOH A 24 624 618 HOH HOH . E 4 HOH B 1 801 617 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O OAB B05 . . . C 3 -17.993 19.292 -28.723 1 75.78 ? OAB B05 501 A 1 HETATM 2 O OAC B05 . . . C 3 -18.421 18.161 -26.637 1 91.64 ? OAC B05 501 A 1 HETATM 3 C CAZ B05 . . . C 3 -21.388 20.965 -25.822 1 79.07 ? CAZ B05 501 A 1 HETATM 4 C CAK B05 . . . C 3 -24.266 26.442 -24.369 1 84.55 ? CAK B05 501 A 1 HETATM 5 C CAJ B05 . . . C 3 -25.892 24.876 -25.21 1 78.18 ? CAJ B05 501 A 1 HETATM 6 C CAI B05 . . . C 3 -22.474 22.616 -19.652 1 74.93 ? CAI B05 501 A 1 HETATM 7 N NBA B05 . . . C 3 -18.747 19.148 -27.562 1 82 ? NBA B05 501 A 1 HETATM 8 C CAY B05 . . . C 3 -22.819 23.379 -21.925 1 77.15 ? CAY B05 501 A 1 HETATM 9 C CAX B05 . . . C 3 -22.287 22.206 -22.43 1 75.12 ? CAX B05 501 A 1 HETATM 10 C CAW B05 . . . C 3 -19.835 19.997 -27.325 1 75.39 ? CAW B05 501 A 1 HETATM 11 C CAV B05 . . . C 3 -21.979 21.688 -26.876 1 76.96 ? CAV B05 501 A 1 HETATM 12 C CAU B05 . . . C 3 -24.973 25.245 -24.23 1 80.96 ? CAU B05 501 A 1 HETATM 13 C CAT B05 . . . C 3 -21.792 20.974 -24.372 1 75.68 ? CAT B05 501 A 1 HETATM 14 C CAQ B05 . . . C 3 -24.692 24.362 -23.037 1 80.59 ? CAQ B05 501 A 1 HETATM 15 C CAP B05 . . . C 3 -20.318 20.13 -26.064 1 76.61 ? CAP B05 501 A 1 HETATM 16 C CAO B05 . . . C 3 -22.921 23.58 -20.548 1 80.42 ? CAO B05 501 A 1 HETATM 17 C CAN B05 . . . C 3 -20.397 20.704 -28.382 1 77.43 ? CAN B05 501 A 1 HETATM 18 C CAM B05 . . . C 3 -21.474 21.553 -28.162 1 78.4 ? CAM B05 501 A 1 HETATM 19 C CAL B05 . . . C 3 -21.831 21.248 -21.521 1 76.49 ? CAL B05 501 A 1 HETATM 20 O OAA B05 . . . C 3 -21.677 19.925 -23.752 1 77.49 ? OAA B05 501 A 1 HETATM 21 N NAR B05 . . . C 3 -22.213 22.083 -23.781 1 76.32 ? NAR B05 501 A 1 HETATM 22 C CAH B05 . . . C 3 -21.934 21.447 -20.152 1 78.82 ? CAH B05 501 A 1 HETATM 23 O OAS B05 . . . C 3 -23.287 24.34 -22.778 1 75.2 ? OAS B05 501 A 1 HETATM 24 C CAF B05 . . . C 3 -26.115 25.707 -26.308 1 74.03 ? CAF B05 501 A 1 HETATM 25 C CAE B05 . . . C 3 -25.409 26.906 -26.425 1 76.67 ? CAE B05 501 A 1 HETATM 26 C CAG B05 . . . C 3 -24.475 27.285 -25.46 1 79.22 ? CAG B05 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #