data_5GQL # _model_server_result.job_id rdQ5nS92n97TWWqbjr1sOA _model_server_result.datetime_utc '2025-07-07 16:53:31' _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 5gql # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5GQL # _exptl.entry_id 5GQL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 5GQL _cell.length_a 103.328 _cell.length_b 103.328 _cell.length_c 103.328 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GQL _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 _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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 103.328 103.328 0 3 'crystal symmetry operation' 3_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 103.328 0 103.328 4 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 103.328 103.328 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_566 z,-x+1,-y+1 0 0 1 -1 0 0 0 -1 0 0 103.328 103.328 7 'crystal symmetry operation' 7_665 -z+1,-x+1,y 0 0 -1 -1 0 0 0 1 0 103.328 103.328 0 8 'crystal symmetry operation' 8_656 -z+1,x,-y+1 0 0 -1 1 0 0 0 -1 0 103.328 0 103.328 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_656 -y+1,z,-x+1 0 -1 0 0 0 1 -1 0 0 103.328 0 103.328 11 'crystal symmetry operation' 11_566 y,-z+1,-x+1 0 1 0 0 0 -1 -1 0 0 0 103.328 103.328 12 'crystal symmetry operation' 12_665 -y+1,-z+1,x 0 -1 0 0 0 -1 1 0 0 103.328 103.328 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 C MG MG . A MG 302 1_555 F O1A ATP . A ATP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 C MG MG . A MG 302 1_555 F O3G ATP . A ATP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc3 C MG MG . A MG 302 1_555 F O1B ATP . A ATP 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc4 C MG MG . A MG 302 1_555 H O HOH . A HOH 434 19_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc5 D MG MG . A MG 303 1_555 E O3G CTP . A CTP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc6 D MG MG . A MG 303 1_555 E O2A CTP . A CTP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc7 D MG MG . A MG 303 1_555 E O2B CTP . A CTP 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc8 D MG MG . A MG 303 1_555 H O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 N1 C2 CTP sing 125 n n N1 C6 CTP sing 126 n n N1 C1' CTP sing 127 n n C2 N3 CTP sing 128 n n C2 O2 CTP doub 129 n n N3 C4 CTP doub 130 n n C4 C5 CTP sing 131 n n C4 N4 CTP sing 132 n n C5 C6 CTP doub 133 n n C5 H5 CTP sing 134 n n C6 H6 CTP sing 135 n n N4 HN41 CTP sing 136 n n N4 HN42 CTP sing 137 n n C1' C2' CTP sing 138 n n C1' O4' CTP sing 139 n n C1' H1' CTP sing 140 n n C2' O2' CTP sing 141 n n C2' C3' CTP sing 142 n n C2' H2' CTP sing 143 n n O2' HO2' CTP sing 144 n n C3' C4' CTP sing 145 n n C3' O3' CTP sing 146 n n C3' H3' CTP sing 147 n n C4' O4' CTP sing 148 n n C4' C5' CTP sing 149 n n C4' H4' CTP sing 150 n n O3' HO3' CTP sing 151 n n C5' O5' CTP sing 152 n n C5' "H5'1" CTP sing 153 n n C5' "H5'2" CTP sing 154 n n O5' PA CTP sing 155 n n PA O1A CTP doub 156 n n PA O2A CTP sing 157 n n PA O3A CTP sing 158 n n O2A HOA2 CTP sing 159 n n O3A PB CTP sing 160 n n PB O1B CTP doub 161 n n PB O2B CTP sing 162 n n PB O3B CTP sing 163 n n O2B HOB2 CTP sing 164 n n O3B PG CTP sing 165 n n PG O1G CTP doub 166 n n PG O2G CTP sing 167 n n PG O3G CTP sing 168 n n O2G HOG2 CTP sing 169 n n O3G HOG3 CTP sing 170 n n # _atom_sites.entry_id 5GQL _atom_sites.fract_transf_matrix[1][1] 0.009678 _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] 0.009678 _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] 0.009678 _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 CTP A 1 304 304 CTP CTP . F 5 ATP A 1 305 305 ATP ATP . G 6 EDO A 1 306 306 EDO EDO . H 7 HOH A 1 401 401 HOH HOH . H 7 HOH A 2 402 402 HOH HOH . H 7 HOH A 3 403 404 HOH HOH . H 7 HOH A 4 404 403 HOH HOH . H 7 HOH A 5 405 405 HOH HOH . H 7 HOH A 6 406 406 HOH HOH . H 7 HOH A 7 407 408 HOH HOH . H 7 HOH A 8 408 407 HOH HOH . H 7 HOH A 9 409 409 HOH HOH . H 7 HOH A 10 410 410 HOH HOH . H 7 HOH A 11 411 411 HOH HOH . H 7 HOH A 12 412 415 HOH HOH . H 7 HOH A 13 413 413 HOH HOH . H 7 HOH A 14 414 414 HOH HOH . H 7 HOH A 15 415 412 HOH HOH . H 7 HOH A 16 416 416 HOH HOH . H 7 HOH A 17 417 417 HOH HOH . H 7 HOH A 18 418 420 HOH HOH . H 7 HOH A 19 419 418 HOH HOH . H 7 HOH A 20 420 422 HOH HOH . H 7 HOH A 21 421 419 HOH HOH . H 7 HOH A 22 422 421 HOH HOH . H 7 HOH A 23 423 424 HOH HOH . H 7 HOH A 24 424 428 HOH HOH . H 7 HOH A 25 425 423 HOH HOH . H 7 HOH A 26 426 426 HOH HOH . H 7 HOH A 27 427 425 HOH HOH . H 7 HOH A 28 428 430 HOH HOH . H 7 HOH A 29 429 431 HOH HOH . H 7 HOH A 30 430 427 HOH HOH . H 7 HOH A 31 431 429 HOH HOH . H 7 HOH A 32 432 432 HOH HOH . H 7 HOH A 33 433 435 HOH HOH . H 7 HOH A 34 434 434 HOH HOH . H 7 HOH A 35 435 433 HOH HOH . H 7 HOH A 36 436 437 HOH HOH . H 7 HOH A 37 437 436 HOH HOH . H 7 HOH A 38 438 440 HOH HOH . H 7 HOH A 39 439 441 HOH HOH . H 7 HOH A 40 440 445 HOH HOH . H 7 HOH A 41 441 442 HOH HOH . H 7 HOH A 42 442 443 HOH HOH . H 7 HOH A 43 443 438 HOH HOH . H 7 HOH A 44 444 439 HOH HOH . H 7 HOH A 45 445 448 HOH HOH . H 7 HOH A 46 446 452 HOH HOH . H 7 HOH A 47 447 444 HOH HOH . H 7 HOH A 48 448 447 HOH HOH . H 7 HOH A 49 449 446 HOH HOH . H 7 HOH A 50 450 450 HOH HOH . H 7 HOH A 51 451 449 HOH HOH . H 7 HOH A 52 452 451 HOH HOH . H 7 HOH A 53 453 454 HOH HOH . H 7 HOH A 54 454 459 HOH HOH . H 7 HOH A 55 455 453 HOH HOH . H 7 HOH A 56 456 455 HOH HOH . H 7 HOH A 57 457 456 HOH HOH . H 7 HOH A 58 458 457 HOH HOH . H 7 HOH A 59 459 458 HOH HOH . H 7 HOH A 60 460 467 HOH HOH . H 7 HOH A 61 461 466 HOH HOH . H 7 HOH A 62 462 461 HOH HOH . H 7 HOH A 63 463 465 HOH HOH . H 7 HOH A 64 464 460 HOH HOH . H 7 HOH A 65 465 462 HOH HOH . H 7 HOH A 66 466 464 HOH HOH . H 7 HOH A 67 467 463 HOH HOH . H 7 HOH A 68 468 469 HOH HOH . H 7 HOH A 69 469 468 HOH HOH . H 7 HOH A 70 470 472 HOH HOH . H 7 HOH A 71 471 470 HOH HOH . H 7 HOH A 72 472 471 HOH HOH . H 7 HOH A 73 473 473 HOH HOH . H 7 HOH A 74 474 474 HOH HOH . H 7 HOH A 75 475 476 HOH HOH . H 7 HOH A 76 476 475 HOH HOH . H 7 HOH A 77 477 481 HOH HOH . H 7 HOH A 78 478 479 HOH HOH . H 7 HOH A 79 479 478 HOH HOH . H 7 HOH A 80 480 483 HOH HOH . H 7 HOH A 81 481 477 HOH HOH . H 7 HOH A 82 482 484 HOH HOH . H 7 HOH A 83 483 482 HOH HOH . H 7 HOH A 84 484 485 HOH HOH . H 7 HOH A 85 485 480 HOH HOH . H 7 HOH A 86 486 488 HOH HOH . H 7 HOH A 87 487 487 HOH HOH . H 7 HOH A 88 488 489 HOH HOH . H 7 HOH A 89 489 492 HOH HOH . H 7 HOH A 90 490 486 HOH HOH . H 7 HOH A 91 491 490 HOH HOH . H 7 HOH A 92 492 491 HOH HOH . H 7 HOH A 93 493 493 HOH HOH . H 7 HOH A 94 494 494 HOH HOH . H 7 HOH A 95 495 495 HOH HOH . H 7 HOH A 96 496 496 HOH HOH . H 7 HOH A 97 497 497 HOH HOH . H 7 HOH A 98 498 498 HOH HOH . H 7 HOH A 99 499 501 HOH HOH . H 7 HOH A 100 500 502 HOH HOH . H 7 HOH A 101 501 503 HOH HOH . H 7 HOH A 102 502 500 HOH HOH . H 7 HOH A 103 503 499 HOH HOH . H 7 HOH A 104 504 505 HOH HOH . H 7 HOH A 105 505 506 HOH HOH . H 7 HOH A 106 506 504 HOH HOH . H 7 HOH A 107 507 520 HOH HOH . H 7 HOH A 108 508 507 HOH HOH . H 7 HOH A 109 509 510 HOH HOH . H 7 HOH A 110 510 509 HOH HOH . H 7 HOH A 111 511 522 HOH HOH . H 7 HOH A 112 512 511 HOH HOH . H 7 HOH A 113 513 508 HOH HOH . H 7 HOH A 114 514 512 HOH HOH . H 7 HOH A 115 515 513 HOH HOH . H 7 HOH A 116 516 516 HOH HOH . H 7 HOH A 117 517 515 HOH HOH . H 7 HOH A 118 518 514 HOH HOH . H 7 HOH A 119 519 517 HOH HOH . H 7 HOH A 120 520 518 HOH HOH . H 7 HOH A 121 521 519 HOH HOH . H 7 HOH A 122 522 521 HOH HOH . H 7 HOH A 123 523 523 HOH HOH . H 7 HOH A 124 524 524 HOH HOH . H 7 HOH A 125 525 526 HOH HOH . H 7 HOH A 126 526 525 HOH HOH . H 7 HOH A 127 527 527 HOH HOH . H 7 HOH A 128 528 528 HOH HOH . H 7 HOH A 129 529 529 HOH HOH . H 7 HOH A 130 530 530 HOH HOH . H 7 HOH A 131 531 531 HOH HOH . H 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 N N1 CTP . . . E 4 43.087 58.489 39.705 1 34.22 ? N1 CTP 304 A 1 HETATM 2 C C2 CTP . . . E 4 42.07 59.448 39.572 1 37.22 ? C2 CTP 304 A 1 HETATM 3 N N3 CTP . . . E 4 41.345 59.546 38.383 1 37.84 ? N3 CTP 304 A 1 HETATM 4 C C4 CTP . . . E 4 41.86 58.969 37.226 1 34.68 ? C4 CTP 304 A 1 HETATM 5 C C5 CTP . . . E 4 42.98 58.123 37.325 1 33.88 ? C5 CTP 304 A 1 HETATM 6 C C6 CTP . . . E 4 43.539 57.833 38.579 1 32.54 ? C6 CTP 304 A 1 HETATM 7 O O2 CTP . . . E 4 41.807 60.238 40.486 1 40.13 ? O2 CTP 304 A 1 HETATM 8 N N4 CTP . . . E 4 41.272 59.214 36.054 1 31.62 ? N4 CTP 304 A 1 HETATM 9 C C1' CTP . . . E 4 43.655 58.213 41.059 1 33.83 ? C1' CTP 304 A 1 HETATM 10 C C2' CTP . . . E 4 42.816 57.196 41.837 1 34.44 ? C2' CTP 304 A 1 HETATM 11 O O2' CTP . . . E 4 42.332 57.824 43.005 1 36.24 ? O2' CTP 304 A 1 HETATM 12 C C3' CTP . . . E 4 43.773 56.092 42.235 1 33.1 ? C3' CTP 304 A 1 HETATM 13 C C4' CTP . . . E 4 45.169 56.638 41.939 1 32.37 ? C4' CTP 304 A 1 HETATM 14 O O4' CTP . . . E 4 45 57.749 41.065 1 31.83 ? O4' CTP 304 A 1 HETATM 15 O O3' CTP . . . E 4 43.668 55.766 43.602 1 36.17 ? O3' CTP 304 A 1 HETATM 16 C C5' CTP . . . E 4 46.045 55.562 41.301 1 28.95 ? C5' CTP 304 A 1 HETATM 17 O O5' CTP . . . E 4 45.539 55.336 39.997 1 27.39 ? O5' CTP 304 A 1 HETATM 18 P PA CTP . . . E 4 45.111 53.905 39.36 1 24.89 ? PA CTP 304 A 1 HETATM 19 O O1A CTP . . . E 4 44.324 54.184 38.1 1 20.91 ? O1A CTP 304 A 1 HETATM 20 O O2A CTP . . . E 4 44.282 52.98 40.245 1 25.04 ? O2A CTP 304 A 1 HETATM 21 O O3A CTP . . . E 4 46.576 53.27 38.988 1 25.69 ? O3A CTP 304 A 1 HETATM 22 P PB CTP . . . E 4 47.504 52.359 39.969 1 24.38 ? PB CTP 304 A 1 HETATM 23 O O1B CTP . . . E 4 48.93 52.854 39.832 1 25.64 ? O1B CTP 304 A 1 HETATM 24 O O2B CTP . . . E 4 47.046 52.45 41.411 1 24.83 ? O2B CTP 304 A 1 HETATM 25 O O3B CTP . . . E 4 47.427 50.849 39.368 1 23.24 ? O3B CTP 304 A 1 HETATM 26 P PG CTP . . . E 4 46.504 49.639 39.983 1 22.61 ? PG CTP 304 A 1 HETATM 27 O O1G CTP . . . E 4 46.133 48.754 38.811 1 21.35 ? O1G CTP 304 A 1 HETATM 28 O O2G CTP . . . E 4 47.319 48.875 41.009 1 22.31 ? O2G CTP 304 A 1 HETATM 29 O O3G CTP . . . E 4 45.239 50.219 40.555 1 22.85 ? O3G CTP 304 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #