data_7RGD # _model_server_result.job_id bKTflx8VH-vP-mStaUbuiQ _model_server_result.datetime_utc '2024-11-23 12:55:19' _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 7rgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":605}' # _entry.id 7RGD # _exptl.entry_id 7RGD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 663.425 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 8 _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 7RGD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RGD _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 M N N ? 5 R N N ? 5 W N N ? 5 BA N N ? 5 GA N N ? 5 LA N N ? 5 QA N N ? 5 VA N N # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 372 n n PA O2A NAD sing 373 n n PA O5B NAD sing 374 n n PA O3 NAD sing 375 n n O2A HOA2 NAD sing 376 n n O5B C5B NAD sing 377 n n C5B C4B NAD sing 378 n n C5B H51A NAD sing 379 n n C5B H52A NAD sing 380 n n C4B O4B NAD sing 381 n n C4B C3B NAD sing 382 n n C4B H4B NAD sing 383 n n O4B C1B NAD sing 384 n n C3B O3B NAD sing 385 n n C3B C2B NAD sing 386 n n C3B H3B NAD sing 387 n n O3B HO3A NAD sing 388 n n C2B O2B NAD sing 389 n n C2B C1B NAD sing 390 n n C2B H2B NAD sing 391 n n O2B HO2A NAD sing 392 n n C1B N9A NAD sing 393 n n C1B H1B NAD sing 394 n n N9A C8A NAD sing 395 n y N9A C4A NAD sing 396 n y C8A N7A NAD doub 397 n y C8A H8A NAD sing 398 n n N7A C5A NAD sing 399 n y C5A C6A NAD sing 400 n y C5A C4A NAD doub 401 n y C6A N6A NAD sing 402 n n C6A N1A NAD doub 403 n y N6A H61A NAD sing 404 n n N6A H62A NAD sing 405 n n N1A C2A NAD sing 406 n y C2A N3A NAD doub 407 n y C2A H2A NAD sing 408 n n N3A C4A NAD sing 409 n y O3 PN NAD sing 410 n n PN O1N NAD doub 411 n n PN O2N NAD sing 412 n n PN O5D NAD sing 413 n n O5D C5D NAD sing 414 n n C5D C4D NAD sing 415 n n C5D H51N NAD sing 416 n n C5D H52N NAD sing 417 n n C4D O4D NAD sing 418 n n C4D C3D NAD sing 419 n n C4D H4D NAD sing 420 n n O4D C1D NAD sing 421 n n C3D O3D NAD sing 422 n n C3D C2D NAD sing 423 n n C3D H3D NAD sing 424 n n O3D HO3N NAD sing 425 n n C2D O2D NAD sing 426 n n C2D C1D NAD sing 427 n n C2D H2D NAD sing 428 n n O2D HO2N NAD sing 429 n n C1D N1N NAD sing 430 n n C1D H1D NAD sing 431 n n N1N C2N NAD sing 432 n y N1N C6N NAD doub 433 n y C2N C3N NAD doub 434 n y C2N H2N NAD sing 435 n n C3N C7N NAD sing 436 n n C3N C4N NAD sing 437 n y C7N O7N NAD doub 438 n n C7N N7N NAD sing 439 n n N7N H71N NAD sing 440 n n N7N H72N NAD sing 441 n n C4N C5N NAD doub 442 n y C4N H4N NAD sing 443 n n C5N C6N NAD sing 444 n y C5N H5N NAD sing 445 n n C6N H6N NAD sing 446 n n # _atom_sites.entry_id 7RGD _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 I 2 GTP A 1 601 601 GTP GTP . J 2 GTP A 1 602 602 GTP GTP . K 3 ATP A 1 603 603 ATP ATP . L 4 IMP A 1 604 604 IMP IMP . M 5 NAD A 1 605 605 NAD NAD . N 2 GTP B 1 601 601 GTP GTP . O 2 GTP B 1 602 602 GTP GTP . P 3 ATP B 1 603 603 ATP ATP . Q 4 IMP B 1 604 604 IMP IMP . R 5 NAD B 1 605 605 NAD NAD . S 2 GTP C 1 601 601 GTP GTP . T 2 GTP C 1 602 602 GTP GTP . U 3 ATP C 1 603 603 ATP ATP . V 4 IMP C 1 604 604 IMP IMP . W 5 NAD C 1 605 605 NAD NAD . X 2 GTP D 1 601 601 GTP GTP . Y 2 GTP D 1 602 602 GTP GTP . Z 3 ATP D 1 603 603 ATP ATP . AA 4 IMP D 1 604 604 IMP IMP . BA 5 NAD D 1 605 605 NAD NAD . CA 2 GTP E 1 601 601 GTP GTP . DA 2 GTP E 1 602 602 GTP GTP . EA 3 ATP E 1 603 603 ATP ATP . FA 4 IMP E 1 604 604 IMP IMP . GA 5 NAD E 1 605 605 NAD NAD . HA 2 GTP F 1 601 601 GTP GTP . IA 2 GTP F 1 602 602 GTP GTP . JA 3 ATP F 1 603 603 ATP ATP . KA 4 IMP F 1 604 604 IMP IMP . LA 5 NAD F 1 605 605 NAD NAD . MA 2 GTP G 1 601 601 GTP GTP . NA 2 GTP G 1 602 602 GTP GTP . OA 3 ATP G 1 603 603 ATP ATP . PA 4 IMP G 1 604 604 IMP IMP . QA 5 NAD G 1 605 605 NAD NAD . RA 2 GTP H 1 601 601 GTP GTP . SA 2 GTP H 1 602 602 GTP GTP . TA 3 ATP H 1 603 603 ATP ATP . UA 4 IMP H 1 604 604 IMP IMP . VA 5 NAD H 1 605 605 NAD NAD . # 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 NAD . . . M 5 145.918 142.225 146.525 1 42.88 ? PA NAD 605 A 1 HETATM 2 O O1A NAD . . . M 5 145.523 142.916 145.283 1 42.88 ? O1A NAD 605 A 1 HETATM 3 O O2A NAD . . . M 5 144.946 141.271 147.097 1 42.88 ? O2A NAD 605 A 1 HETATM 4 O O5B NAD . . . M 5 147.241 141.383 146.192 1 42.88 ? O5B NAD 605 A 1 HETATM 5 C C5B NAD . . . M 5 147.904 140.556 147.131 1 42.88 ? C5B NAD 605 A 1 HETATM 6 C C4B NAD . . . M 5 148.566 139.365 146.426 1 42.88 ? C4B NAD 605 A 1 HETATM 7 O O4B NAD . . . M 5 147.573 138.398 146.128 1 42.88 ? O4B NAD 605 A 1 HETATM 8 C C3B NAD . . . M 5 149.261 139.724 145.105 1 42.88 ? C3B NAD 605 A 1 HETATM 9 O O3B NAD . . . M 5 150.419 138.91 144.967 1 42.88 ? O3B NAD 605 A 1 HETATM 10 C C2B NAD . . . M 5 148.171 139.385 144.078 1 42.88 ? C2B NAD 605 A 1 HETATM 11 O O2B NAD . . . M 5 148.664 139.134 142.767 1 42.88 ? O2B NAD 605 A 1 HETATM 12 C C1B NAD . . . M 5 147.532 138.16 144.733 1 42.88 ? C1B NAD 605 A 1 HETATM 13 N N9A NAD . . . M 5 146.133 137.879 144.328 1 42.88 ? N9A NAD 605 A 1 HETATM 14 C C8A NAD . . . M 5 145.047 138.717 144.292 1 42.88 ? C8A NAD 605 A 1 HETATM 15 N N7A NAD . . . M 5 143.936 138.148 143.894 1 42.88 ? N7A NAD 605 A 1 HETATM 16 C C5A NAD . . . M 5 144.334 136.827 143.665 1 42.88 ? C5A NAD 605 A 1 HETATM 17 C C6A NAD . . . M 5 143.68 135.647 143.24 1 42.88 ? C6A NAD 605 A 1 HETATM 18 N N6A NAD . . . M 5 142.406 135.546 142.925 1 42.88 ? N6A NAD 605 A 1 HETATM 19 N N1A NAD . . . M 5 144.331 134.495 143.134 1 42.88 ? N1A NAD 605 A 1 HETATM 20 C C2A NAD . . . M 5 145.624 134.488 143.418 1 42.88 ? C2A NAD 605 A 1 HETATM 21 N N3A NAD . . . M 5 146.371 135.504 143.825 1 42.88 ? N3A NAD 605 A 1 HETATM 22 C C4A NAD . . . M 5 145.656 136.658 143.927 1 42.88 ? C4A NAD 605 A 1 HETATM 23 O O3 NAD . . . M 5 146.148 143.304 147.651 1 42.88 ? O3 NAD 605 A 1 HETATM 24 P PN NAD . . . M 5 147.492 144.128 147.614 1 42.88 ? PN NAD 605 A 1 HETATM 25 O O1N NAD . . . M 5 147.86 144.558 146.257 1 42.88 ? O1N NAD 605 A 1 HETATM 26 O O2N NAD . . . M 5 148.487 143.455 148.473 1 42.88 ? O2N NAD 605 A 1 HETATM 27 O O5D NAD . . . M 5 147.005 145.437 148.417 1 42.88 ? O5D NAD 605 A 1 HETATM 28 C C5D NAD . . . M 5 146.581 145.32 149.768 1 42.88 ? C5D NAD 605 A 1 HETATM 29 C C4D NAD . . . M 5 145.986 146.608 150.354 1 42.88 ? C4D NAD 605 A 1 HETATM 30 O O4D NAD . . . M 5 146.98 147.615 150.498 1 42.88 ? O4D NAD 605 A 1 HETATM 31 C C3D NAD . . . M 5 144.872 147.208 149.498 1 42.88 ? C3D NAD 605 A 1 HETATM 32 O O3D NAD . . . M 5 143.992 147.906 150.356 1 42.88 ? O3D NAD 605 A 1 HETATM 33 C C2D NAD . . . M 5 145.643 148.166 148.595 1 42.88 ? C2D NAD 605 A 1 HETATM 34 O O2D NAD . . . M 5 144.889 149.277 148.114 1 42.88 ? O2D NAD 605 A 1 HETATM 35 C C1D NAD . . . M 5 146.781 148.625 149.52 1 42.88 ? C1D NAD 605 A 1 HETATM 36 N N1N NAD . . . M 5 148.021 148.954 148.763 1 42.88 ? N1N NAD 605 A 1 HETATM 37 C C2N NAD . . . M 5 148.011 149.993 147.888 1 42.88 ? C2N NAD 605 A 1 HETATM 38 C C3N NAD . . . M 5 149.153 150.331 147.129 1 42.88 ? C3N NAD 605 A 1 HETATM 39 C C7N NAD . . . M 5 149.163 151.39 146.197 1 42.88 ? C7N NAD 605 A 1 HETATM 40 O O7N NAD . . . M 5 150.168 152.05 145.991 1 42.88 ? O7N NAD 605 A 1 HETATM 41 N N7N NAD . . . M 5 148.076 151.62 145.506 1 42.88 ? N7N NAD 605 A 1 HETATM 42 C C4N NAD . . . M 5 150.339 149.609 147.327 1 42.88 ? C4N NAD 605 A 1 HETATM 43 C C5N NAD . . . M 5 150.333 148.553 148.247 1 42.88 ? C5N NAD 605 A 1 HETATM 44 C C6N NAD . . . M 5 149.155 148.227 148.94 1 42.88 ? C6N NAD 605 A 1 HETATM 45 H H51A NAD . . . M 5 147.213 140.185 147.887 1 42.88 ? H51A NAD 605 A 1 HETATM 46 H H52A NAD . . . M 5 148.684 141.127 147.632 1 42.88 ? H52A NAD 605 A 1 HETATM 47 H H4B NAD . . . M 5 149.297 138.932 147.107 1 42.88 ? H4B NAD 605 A 1 HETATM 48 H H3B NAD . . . M 5 149.53 140.779 145.07 1 42.88 ? H3B NAD 605 A 1 HETATM 49 H HO3A NAD . . . M 5 150.889 139.178 144.174 1 42.88 ? HO3A NAD 605 A 1 HETATM 50 H H2B NAD . . . M 5 147.439 140.192 144.051 1 42.88 ? H2B NAD 605 A 1 HETATM 51 H HO2A NAD . . . M 5 148.64 139.953 142.276 1 42.88 ? HO2A NAD 605 A 1 HETATM 52 H H1B NAD . . . M 5 148.155 137.296 144.505 1 42.88 ? H1B NAD 605 A 1 HETATM 53 H H8A NAD . . . M 5 145.112 139.757 144.572 1 42.88 ? H8A NAD 605 A 1 HETATM 54 H H61A NAD . . . M 5 141.801 136.352 142.973 1 42.88 ? H61A NAD 605 A 1 HETATM 55 H H62A NAD . . . M 5 142.069 134.646 142.616 1 42.88 ? H62A NAD 605 A 1 HETATM 56 H H2A NAD . . . M 5 146.129 133.539 143.314 1 42.88 ? H2A NAD 605 A 1 HETATM 57 H H51N NAD . . . M 5 147.425 145.024 150.39 1 42.88 ? H51N NAD 605 A 1 HETATM 58 H H52N NAD . . . M 5 145.824 144.541 149.85 1 42.88 ? H52N NAD 605 A 1 HETATM 59 H H4D NAD . . . M 5 145.586 146.359 151.336 1 42.88 ? H4D NAD 605 A 1 HETATM 60 H H3D NAD . . . M 5 144.348 146.445 148.923 1 42.88 ? H3D NAD 605 A 1 HETATM 61 H HO3N NAD . . . M 5 143.118 147.864 149.964 1 42.88 ? HO3N NAD 605 A 1 HETATM 62 H H2D NAD . . . M 5 146.05 147.605 147.754 1 42.88 ? H2D NAD 605 A 1 HETATM 63 H HO2N NAD . . . M 5 143.971 149.028 147.986 1 42.88 ? HO2N NAD 605 A 1 HETATM 64 H H1D NAD . . . M 5 146.441 149.519 150.042 1 42.88 ? H1D NAD 605 A 1 HETATM 65 H H2N NAD . . . M 5 147.089 150.549 147.8 1 42.88 ? H2N NAD 605 A 1 HETATM 66 H H71N NAD . . . M 5 148.104 152.383 144.848 1 42.88 ? H71N NAD 605 A 1 HETATM 67 H H72N NAD . . . M 5 147.246 151.061 145.627 1 42.88 ? H72N NAD 605 A 1 HETATM 68 H H4N NAD . . . M 5 151.235 149.844 146.772 1 42.88 ? H4N NAD 605 A 1 HETATM 69 H H5N NAD . . . M 5 151.228 147.966 148.386 1 42.88 ? H5N NAD 605 A 1 HETATM 70 H H6N NAD . . . M 5 149.131 147.382 149.611 1 42.88 ? H6N NAD 605 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 308 _model_server_stats.query_time_ms 390 _model_server_stats.encode_time_ms 35 _model_server_stats.element_count 70 #