data_5GQJ # _model_server_result.job_id d_On0Y-RtBPXrDKGdTa3ow _model_server_result.datetime_utc '2025-07-21 16:49:44' _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 5gqj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5GQJ # _exptl.entry_id 5GQJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 5GQJ _cell.length_a 103.06 _cell.length_b 103.06 _cell.length_c 103.06 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GQJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 covale ? covale1 A C ACE 1 A ACE 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc1 C MG MG . A MG 302 1_555 F O1A CTP . A CTP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc2 C MG MG . A MG 302 1_555 F O1G CTP . A CTP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc3 C MG MG . A MG 302 1_555 F O1B CTP . A CTP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc4 C MG MG . A MG 302 1_555 J O HOH . A HOH 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 D MG MG . A MG 303 1_555 E O2B ATP . A ATP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc6 D MG MG . A MG 303 1_555 E O2G ATP . A ATP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc7 D MG MG . A MG 303 1_555 E O2A ATP . A ATP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc8 D MG MG . A MG 303 1_555 J O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc9 D MG MG . A MG 303 1_555 J O HOH . A HOH 417 18_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 76 n n PG O2G ATP sing 77 n n PG O3G ATP sing 78 n n PG O3B ATP sing 79 n n O2G HOG2 ATP sing 80 n n O3G HOG3 ATP sing 81 n n PB O1B ATP doub 82 n n PB O2B ATP sing 83 n n PB O3B ATP sing 84 n n PB O3A ATP sing 85 n n O2B HOB2 ATP sing 86 n n PA O1A ATP doub 87 n n PA O2A ATP sing 88 n n PA O3A ATP sing 89 n n PA O5' ATP sing 90 n n O2A HOA2 ATP sing 91 n n O5' C5' ATP sing 92 n n C5' C4' ATP sing 93 n n C5' "H5'1" ATP sing 94 n n C5' "H5'2" ATP sing 95 n n C4' O4' ATP sing 96 n n C4' C3' ATP sing 97 n n C4' H4' ATP sing 98 n n O4' C1' ATP sing 99 n n C3' O3' ATP sing 100 n n C3' C2' ATP sing 101 n n C3' H3' ATP sing 102 n n O3' HO3' ATP sing 103 n n C2' O2' ATP sing 104 n n C2' C1' ATP sing 105 n n C2' H2' ATP sing 106 n n O2' HO2' ATP sing 107 n n C1' N9 ATP sing 108 n n C1' H1' ATP sing 109 n n N9 C8 ATP sing 110 n y N9 C4 ATP sing 111 n y C8 N7 ATP doub 112 n y C8 H8 ATP sing 113 n n N7 C5 ATP sing 114 n y C5 C6 ATP sing 115 n y C5 C4 ATP doub 116 n y C6 N6 ATP sing 117 n n C6 N1 ATP doub 118 n y N6 HN61 ATP sing 119 n n N6 HN62 ATP sing 120 n n N1 C2 ATP sing 121 n y C2 N3 ATP doub 122 n y C2 H2 ATP sing 123 n n N3 C4 ATP sing 124 n y # _atom_sites.entry_id 5GQJ _atom_sites.fract_transf_matrix[1][1] 0.009703 _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] 0.009703 _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] 0.009703 _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 B 2 CL A 1 301 301 CL CL . C 3 MG A 1 302 302 MG MG . D 3 MG A 1 303 303 MG MG . E 4 ATP A 1 304 304 ATP ATP . F 5 CTP A 1 305 305 CTP CTP . G 6 EDO A 1 306 306 EDO EDO . H 6 EDO A 1 307 307 EDO EDO . I 6 EDO A 1 308 308 EDO EDO . J 7 HOH A 1 401 401 HOH HOH . J 7 HOH A 2 402 402 HOH HOH . J 7 HOH A 3 403 404 HOH HOH . J 7 HOH A 4 404 405 HOH HOH . J 7 HOH A 5 405 407 HOH HOH . J 7 HOH A 6 406 408 HOH HOH . J 7 HOH A 7 407 411 HOH HOH . J 7 HOH A 8 408 409 HOH HOH . J 7 HOH A 9 409 413 HOH HOH . J 7 HOH A 10 410 412 HOH HOH . J 7 HOH A 11 411 410 HOH HOH . J 7 HOH A 12 412 403 HOH HOH . J 7 HOH A 13 413 406 HOH HOH . J 7 HOH A 14 414 414 HOH HOH . J 7 HOH A 15 415 416 HOH HOH . J 7 HOH A 16 416 420 HOH HOH . J 7 HOH A 17 417 415 HOH HOH . J 7 HOH A 18 418 419 HOH HOH . J 7 HOH A 19 419 423 HOH HOH . J 7 HOH A 20 420 426 HOH HOH . J 7 HOH A 21 421 417 HOH HOH . J 7 HOH A 22 422 422 HOH HOH . J 7 HOH A 23 423 418 HOH HOH . J 7 HOH A 24 424 425 HOH HOH . J 7 HOH A 25 425 424 HOH HOH . J 7 HOH A 26 426 428 HOH HOH . J 7 HOH A 27 427 421 HOH HOH . J 7 HOH A 28 428 435 HOH HOH . J 7 HOH A 29 429 437 HOH HOH . J 7 HOH A 30 430 431 HOH HOH . J 7 HOH A 31 431 433 HOH HOH . J 7 HOH A 32 432 434 HOH HOH . J 7 HOH A 33 433 441 HOH HOH . J 7 HOH A 34 434 429 HOH HOH . J 7 HOH A 35 435 430 HOH HOH . J 7 HOH A 36 436 432 HOH HOH . J 7 HOH A 37 437 436 HOH HOH . J 7 HOH A 38 438 438 HOH HOH . J 7 HOH A 39 439 444 HOH HOH . J 7 HOH A 40 440 427 HOH HOH . J 7 HOH A 41 441 440 HOH HOH . J 7 HOH A 42 442 439 HOH HOH . J 7 HOH A 43 443 443 HOH HOH . J 7 HOH A 44 444 447 HOH HOH . J 7 HOH A 45 445 446 HOH HOH . J 7 HOH A 46 446 445 HOH HOH . J 7 HOH A 47 447 451 HOH HOH . J 7 HOH A 48 448 452 HOH HOH . J 7 HOH A 49 449 442 HOH HOH . J 7 HOH A 50 450 450 HOH HOH . J 7 HOH A 51 451 449 HOH HOH . J 7 HOH A 52 452 448 HOH HOH . J 7 HOH A 53 453 453 HOH HOH . J 7 HOH A 54 454 457 HOH HOH . J 7 HOH A 55 455 459 HOH HOH . J 7 HOH A 56 456 460 HOH HOH . J 7 HOH A 57 457 464 HOH HOH . J 7 HOH A 58 458 456 HOH HOH . J 7 HOH A 59 459 455 HOH HOH . J 7 HOH A 60 460 466 HOH HOH . J 7 HOH A 61 461 454 HOH HOH . J 7 HOH A 62 462 458 HOH HOH . J 7 HOH A 63 463 468 HOH HOH . J 7 HOH A 64 464 475 HOH HOH . J 7 HOH A 65 465 463 HOH HOH . J 7 HOH A 66 466 462 HOH HOH . J 7 HOH A 67 467 474 HOH HOH . J 7 HOH A 68 468 461 HOH HOH . J 7 HOH A 69 469 465 HOH HOH . J 7 HOH A 70 470 467 HOH HOH . J 7 HOH A 71 471 478 HOH HOH . J 7 HOH A 72 472 473 HOH HOH . J 7 HOH A 73 473 479 HOH HOH . J 7 HOH A 74 474 469 HOH HOH . J 7 HOH A 75 475 480 HOH HOH . J 7 HOH A 76 476 471 HOH HOH . J 7 HOH A 77 477 476 HOH HOH . J 7 HOH A 78 478 477 HOH HOH . J 7 HOH A 79 479 485 HOH HOH . J 7 HOH A 80 480 484 HOH HOH . J 7 HOH A 81 481 481 HOH HOH . J 7 HOH A 82 482 487 HOH HOH . J 7 HOH A 83 483 488 HOH HOH . J 7 HOH A 84 484 472 HOH HOH . J 7 HOH A 85 485 490 HOH HOH . J 7 HOH A 86 486 482 HOH HOH . J 7 HOH A 87 487 486 HOH HOH . J 7 HOH A 88 488 483 HOH HOH . J 7 HOH A 89 489 494 HOH HOH . J 7 HOH A 90 490 489 HOH HOH . J 7 HOH A 91 491 493 HOH HOH . J 7 HOH A 92 492 492 HOH HOH . J 7 HOH A 93 493 495 HOH HOH . J 7 HOH A 94 494 491 HOH HOH . J 7 HOH A 95 495 496 HOH HOH . J 7 HOH A 96 496 470 HOH HOH . J 7 HOH A 97 497 499 HOH HOH . J 7 HOH A 98 498 498 HOH HOH . J 7 HOH A 99 499 501 HOH HOH . J 7 HOH A 100 500 502 HOH HOH . J 7 HOH A 101 501 504 HOH HOH . J 7 HOH A 102 502 497 HOH HOH . J 7 HOH A 103 503 503 HOH HOH . J 7 HOH A 104 504 509 HOH HOH . J 7 HOH A 105 505 500 HOH HOH . J 7 HOH A 106 506 506 HOH HOH . J 7 HOH A 107 507 505 HOH HOH . J 7 HOH A 108 508 508 HOH HOH . J 7 HOH A 109 509 512 HOH HOH . J 7 HOH A 110 510 510 HOH HOH . J 7 HOH A 111 511 507 HOH HOH . J 7 HOH A 112 512 511 HOH HOH . J 7 HOH A 113 513 523 HOH HOH . J 7 HOH A 114 514 514 HOH HOH . J 7 HOH A 115 515 513 HOH HOH . J 7 HOH A 116 516 517 HOH HOH . J 7 HOH A 117 517 515 HOH HOH . J 7 HOH A 118 518 518 HOH HOH . J 7 HOH A 119 519 521 HOH HOH . J 7 HOH A 120 520 516 HOH HOH . J 7 HOH A 121 521 520 HOH HOH . J 7 HOH A 122 522 522 HOH HOH . J 7 HOH A 123 523 519 HOH HOH . J 7 HOH A 124 524 524 HOH HOH . J 7 HOH A 125 525 525 HOH HOH . J 7 HOH A 126 526 527 HOH HOH . J 7 HOH A 127 527 526 HOH HOH . J 7 HOH A 128 528 528 HOH HOH . J 7 HOH A 129 529 529 HOH HOH . J 7 HOH A 130 530 530 HOH HOH . J 7 HOH A 131 531 531 HOH HOH . J 7 HOH A 132 532 532 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 P PG ATP . . . E 4 24.81 49.268 5.67 1 28.65 ? PG ATP 304 A 1 HETATM 2 O O1G ATP . . . E 4 23.933 48.062 5.379 1 28.4 ? O1G ATP 304 A 1 HETATM 3 O O2G ATP . . . E 4 25.811 49.131 6.812 1 28.19 ? O2G ATP 304 A 1 HETATM 4 O O3G ATP . . . E 4 24.124 50.613 5.657 1 27.04 ? O3G ATP 304 A 1 HETATM 5 P PB ATP . . . E 4 27.164 48.52 4.158 1 23.54 ? PB ATP 304 A 1 HETATM 6 O O1B ATP . . . E 4 27.227 48.314 2.617 1 17.65 ? O1B ATP 304 A 1 HETATM 7 O O2B ATP . . . E 4 27.358 47.452 5.236 1 22.31 ? O2B ATP 304 A 1 HETATM 8 O O3B ATP . . . E 4 25.747 49.331 4.356 1 25.41 ? O3B ATP 304 A 1 HETATM 9 P PA ATP . . . E 4 28.727 50.444 5.787 1 25.6 ? PA ATP 304 A 1 HETATM 10 O O1A ATP . . . E 4 27.862 51.701 5.814 1 26.44 ? O1A ATP 304 A 1 HETATM 11 O O2A ATP . . . E 4 28.643 49.397 6.92 1 26.96 ? O2A ATP 304 A 1 HETATM 12 O O3A ATP . . . E 4 28.197 49.784 4.383 1 22.33 ? O3A ATP 304 A 1 HETATM 13 O O5' ATP . . . E 4 30.266 50.827 5.408 1 25.33 ? O5' ATP 304 A 1 HETATM 14 C C5' ATP . . . E 4 30.562 51.795 4.36 1 27.95 ? C5' ATP 304 A 1 HETATM 15 C C4' ATP . . . E 4 31.998 52.294 4.531 1 35.41 ? C4' ATP 304 A 1 HETATM 16 O O4' ATP . . . E 4 32.064 53.146 5.694 1 38.8 ? O4' ATP 304 A 1 HETATM 17 C C3' ATP . . . E 4 33.027 51.178 4.795 1 36.31 ? C3' ATP 304 A 1 HETATM 18 O O3' ATP . . . E 4 34.29 51.558 4.22 1 36.78 ? O3' ATP 304 A 1 HETATM 19 C C2' ATP . . . E 4 33.168 51.109 6.314 1 42.07 ? C2' ATP 304 A 1 HETATM 20 O O2' ATP . . . E 4 34.433 50.529 6.735 1 39.23 ? O2' ATP 304 A 1 HETATM 21 C C1' ATP . . . E 4 32.897 52.57 6.736 1 42.69 ? C1' ATP 304 A 1 HETATM 22 N N9 ATP . . . E 4 32.227 52.856 8.055 1 44.05 ? N9 ATP 304 A 1 HETATM 23 C C8 ATP . . . E 4 31.479 52.049 8.87 1 45.42 ? C8 ATP 304 A 1 HETATM 24 N N7 ATP . . . E 4 31.021 52.719 9.976 1 41.84 ? N7 ATP 304 A 1 HETATM 25 C C5 ATP . . . E 4 31.482 53.995 9.888 1 43.02 ? C5 ATP 304 A 1 HETATM 26 C C6 ATP . . . E 4 31.398 55.27 10.684 1 45.93 ? C6 ATP 304 A 1 HETATM 27 N N6 ATP . . . E 4 30.718 55.313 11.863 1 45.78 ? N6 ATP 304 A 1 HETATM 28 N N1 ATP . . . E 4 32.021 56.401 10.196 1 43.55 ? N1 ATP 304 A 1 HETATM 29 C C2 ATP . . . E 4 32.715 56.407 9.028 1 46.38 ? C2 ATP 304 A 1 HETATM 30 N N3 ATP . . . E 4 32.838 55.291 8.254 1 46.62 ? N3 ATP 304 A 1 HETATM 31 C C4 ATP . . . E 4 32.267 54.083 8.617 1 45.5 ? C4 ATP 304 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #