data_7VYF # _model_server_result.job_id chfs60W-DCiYkwyAg9g2wA _model_server_result.datetime_utc '2024-11-14 17:29:14' _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 7vyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":402}' # _entry.id 7VYF # _exptl.entry_id 7VYF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 745.421 _entity.id 24 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 7VYF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA _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 ? _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 24 _struct_asym.id AA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_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 _struct_conn.pdbx_value_order disulf ? disulf1 E SG CYS 11 F CYS 24 1_555 E SG CYS 45 F CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 P C HIS 40 Q HIS 117 1_555 P N 2MR 41 Q 2MR 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 P C 2MR 41 Q 2MR 118 1_555 P N GLY 42 Q GLY 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A SG CYS 354 A CYS 379 1_555 S FE4 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 A SG CYS 357 A CYS 382 1_555 S FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 A SG CYS 360 A CYS 385 1_555 S FE3 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc4 A SG CYS 400 A CYS 425 1_555 S FE2 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 B SG CYS 77 B CYS 113 1_555 U FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 B SG CYS 80 B CYS 116 1_555 U FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc7 B SG CYS 83 B CYS 119 1_555 U FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc8 B SG CYS 87 B CYS 123 1_555 V FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc9 B SG CYS 116 B CYS 152 1_555 V FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc10 B SG CYS 119 B CYS 155 1_555 V FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc11 B SG CYS 122 B CYS 158 1_555 V FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc12 B SG CYS 126 B CYS 162 1_555 U FE4 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc13 C SG CYS 31 C CYS 71 1_555 W FE3 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc14 C SG CYS 32 C CYS 72 1_555 W FE2 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc15 C SG CYS 96 C CYS 136 1_555 W FE4 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc16 C SG CYS 126 C CYS 166 1_555 W FE1 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc17 L SG CYS 36 M CYS 64 1_555 EA FE2 FES . M FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc18 L SG CYS 47 M CYS 75 1_555 EA FE2 FES . M FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc19 L SG CYS 50 M CYS 78 1_555 EA FE1 FES . M FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc20 L SG CYS 64 M CYS 92 1_555 EA FE1 FES . M FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc21 L NE2 HIS 96 M HIS 124 1_555 CA FE3 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc22 L SG CYS 100 M CYS 128 1_555 CA FE2 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc23 L SG CYS 103 M CYS 131 1_555 CA FE1 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc24 L SG CYS 109 M CYS 137 1_555 CA FE4 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc25 L SG CYS 148 M CYS 176 1_555 DA FE4 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc26 L SG CYS 151 M CYS 179 1_555 DA FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc27 L SG CYS 154 M CYS 182 1_555 DA FE3 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc28 L O ILE 195 M ILE 223 1_555 FA MG MG . M MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc29 L SG CYS 198 M CYS 226 1_555 DA FE2 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc30 L O CYS 198 M CYS 226 1_555 FA MG MG . M MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc31 L O LEU 203 M LEU 231 1_555 FA MG MG . M MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc32 N SG CYS 103 O CYS 135 1_555 HA FE1 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc33 N SG CYS 108 O CYS 140 1_555 HA FE1 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc34 N SG CYS 144 O CYS 176 1_555 HA FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc35 N SG CYS 148 O CYS 180 1_555 HA FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc36 Q SG CYS 59 T CYS 86 1_555 IA ZN ZN . T ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc37 Q NE2 HIS 68 T HIS 95 1_555 IA ZN ZN . T ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc38 Q SG CYS 84 T CYS 111 1_555 IA ZN ZN . T ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7VYF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 S 19 SF4 A 1 501 501 SF4 SF4 . T 20 FMN A 1 502 502 FMN FMN . U 19 SF4 B 1 301 301 SF4 SF4 . V 19 SF4 B 1 302 302 SF4 SF4 . W 19 SF4 C 1 301 301 SF4 SF4 . X 21 970 C 1 302 501 970 970 . Y 22 8Q1 G 1 201 201 8Q1 8Q1 . Z 23 PEE J 1 401 311 PEE PEE . AA 24 NDP J 1 402 401 NDP NDP . BA 25 UQ J 1 403 402 UQ UQ . CA 19 SF4 M 1 801 801 SF4 SF4 . DA 19 SF4 M 1 802 802 SF4 SF4 . EA 26 FES M 1 803 803 FES FES . FA 27 MG M 1 804 805 MG MG . GA 28 CDL N 1 201 202 CDL CDL . HA 26 FES O 1 301 301 FES FES . IA 29 ZN T 1 201 150 ZN ZN . # 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 P PA NDP . . . AA 24 103.206 155.137 159.075 1 21.92 ? PA NDP 402 J 1 HETATM 2 O O1A NDP . . . AA 24 102.723 155.122 157.653 1 21.92 ? O1A NDP 402 J 1 HETATM 3 O O2A NDP . . . AA 24 104.643 154.687 159.117 1 21.92 ? O2A NDP 402 J 1 HETATM 4 O O5B NDP . . . AA 24 102.264 154.097 159.987 1 21.92 ? O5B NDP 402 J 1 HETATM 5 C C5B NDP . . . AA 24 100.966 154.56 160.383 1 21.92 ? C5B NDP 402 J 1 HETATM 6 C C4B NDP . . . AA 24 100.214 153.426 161.086 1 21.92 ? C4B NDP 402 J 1 HETATM 7 O O4B NDP . . . AA 24 98.966 153.573 160.911 1 21.92 ? O4B NDP 402 J 1 HETATM 8 C C3B NDP . . . AA 24 100.648 151.953 160.451 1 21.92 ? C3B NDP 402 J 1 HETATM 9 O O3B NDP . . . AA 24 100.92 151.016 161.535 1 21.92 ? O3B NDP 402 J 1 HETATM 10 C C2B NDP . . . AA 24 99.691 151.544 159.782 1 21.92 ? C2B NDP 402 J 1 HETATM 11 O O2B NDP . . . AA 24 99.556 150.039 159.956 1 21.92 ? O2B NDP 402 J 1 HETATM 12 C C1B NDP . . . AA 24 98.434 152.248 160.383 1 21.92 ? C1B NDP 402 J 1 HETATM 13 N N9A NDP . . . AA 24 97.533 152.462 159.427 1 21.92 ? N9A NDP 402 J 1 HETATM 14 C C8A NDP . . . AA 24 97.731 153.148 158.322 1 21.92 ? C8A NDP 402 J 1 HETATM 15 N N7A NDP . . . AA 24 96.616 153.158 157.596 1 21.92 ? N7A NDP 402 J 1 HETATM 16 C C5A NDP . . . AA 24 95.69 152.463 158.25 1 21.92 ? C5A NDP 402 J 1 HETATM 17 C C6A NDP . . . AA 24 94.343 152.125 157.995 1 21.92 ? C6A NDP 402 J 1 HETATM 18 N N6A NDP . . . AA 24 93.672 152.579 156.753 1 21.92 ? N6A NDP 402 J 1 HETATM 19 N N1A NDP . . . AA 24 93.69 151.397 158.878 1 21.92 ? N1A NDP 402 J 1 HETATM 20 C C2A NDP . . . AA 24 94.293 150.989 159.994 1 21.92 ? C2A NDP 402 J 1 HETATM 21 N N3A NDP . . . AA 24 95.551 151.283 160.267 1 21.92 ? N3A NDP 402 J 1 HETATM 22 C C4A NDP . . . AA 24 96.274 152.015 159.42 1 21.92 ? C4A NDP 402 J 1 HETATM 23 O O3 NDP . . . AA 24 103.075 156.667 159.686 1 21.92 ? O3 NDP 402 J 1 HETATM 24 P PN NDP . . . AA 24 104.029 157.29 160.897 1 21.92 ? PN NDP 402 J 1 HETATM 25 O O1N NDP . . . AA 24 104.424 156.197 161.861 1 21.92 ? O1N NDP 402 J 1 HETATM 26 O O2N NDP . . . AA 24 105.271 157.906 160.287 1 21.92 ? O2N NDP 402 J 1 HETATM 27 O O5D NDP . . . AA 24 103.197 158.457 161.726 1 21.92 ? O5D NDP 402 J 1 HETATM 28 C C5D NDP . . . AA 24 102.126 158.079 162.563 1 21.92 ? C5D NDP 402 J 1 HETATM 29 C C4D NDP . . . AA 24 101.212 159.26 162.721 1 21.92 ? C4D NDP 402 J 1 HETATM 30 O O4D NDP . . . AA 24 102.109 160.685 162.768 1 21.92 ? O4D NDP 402 J 1 HETATM 31 C C3D NDP . . . AA 24 100.42 159.341 161.728 1 21.92 ? C3D NDP 402 J 1 HETATM 32 O O3D NDP . . . AA 24 99.034 159.635 162.209 1 21.92 ? O3D NDP 402 J 1 HETATM 33 C C2D NDP . . . AA 24 100.932 160.574 160.867 1 21.92 ? C2D NDP 402 J 1 HETATM 34 O O2D NDP . . . AA 24 99.906 161.166 160.274 1 21.92 ? O2D NDP 402 J 1 HETATM 35 C C1D NDP . . . AA 24 101.528 161.504 161.945 1 21.92 ? C1D NDP 402 J 1 HETATM 36 N N1N NDP . . . AA 24 102.52 162.455 161.345 1 21.92 ? N1N NDP 402 J 1 HETATM 37 C C2N NDP . . . AA 24 103.814 161.74 161.129 1 21.92 ? C2N NDP 402 J 1 HETATM 38 C C3N NDP . . . AA 24 105.005 162.728 161.028 1 21.92 ? C3N NDP 402 J 1 HETATM 39 C C7N NDP . . . AA 24 106.014 162.203 159.985 1 21.92 ? C7N NDP 402 J 1 HETATM 40 O O7N NDP . . . AA 24 106.407 161.084 160.053 1 21.92 ? O7N NDP 402 J 1 HETATM 41 N N7N NDP . . . AA 24 106.479 163.074 158.937 1 21.92 ? N7N NDP 402 J 1 HETATM 42 C C4N NDP . . . AA 24 104.57 164.097 160.647 1 21.92 ? C4N NDP 402 J 1 HETATM 43 C C5N NDP . . . AA 24 103.647 164.689 161.674 1 21.92 ? C5N NDP 402 J 1 HETATM 44 C C6N NDP . . . AA 24 102.656 163.641 162.238 1 21.92 ? C6N NDP 402 J 1 HETATM 45 P P2B NDP . . . AA 24 100.047 149.037 158.684 1 21.92 ? P2B NDP 402 J 1 HETATM 46 O O1X NDP . . . AA 24 99.627 147.616 158.981 1 21.92 ? O1X NDP 402 J 1 HETATM 47 O O2X NDP . . . AA 24 99.392 149.484 157.407 1 21.92 ? O2X NDP 402 J 1 HETATM 48 O O3X NDP . . . AA 24 101.552 149.099 158.548 1 21.92 ? O3X NDP 402 J 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #