data_5GQJ # _model_server_result.job_id L2s1lICzf7tMbCGPU3NERA _model_server_result.datetime_utc '2025-07-21 03:33:32' _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":"F","auth_seq_id":305}' # _entry.id 5GQJ # _exptl.entry_id 5GQJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 5 _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 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 5 _struct_asym.id F _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 '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 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 N N1 CTP . . . F 5 -6.963 12.139 -8.783 1 57.65 ? N1 CTP 305 A 1 HETATM 2 C C2 CTP . . . F 5 -7.931 12.324 -9.856 1 55.31 ? C2 CTP 305 A 1 HETATM 3 N N3 CTP . . . F 5 -8.158 13.545 -10.409 1 52.31 ? N3 CTP 305 A 1 HETATM 4 C C4 CTP . . . F 5 -7.467 14.622 -9.971 1 44.96 ? C4 CTP 305 A 1 HETATM 5 C C5 CTP . . . F 5 -6.519 14.469 -8.936 1 40.48 ? C5 CTP 305 A 1 HETATM 6 C C6 CTP . . . F 5 -6.262 13.22 -8.344 1 47.58 ? C6 CTP 305 A 1 HETATM 7 O O2 CTP . . . F 5 -8.637 11.401 -10.325 1 56.81 ? O2 CTP 305 A 1 HETATM 8 N N4 CTP . . . F 5 -7.737 15.804 -10.585 1 37.1 ? N4 CTP 305 A 1 HETATM 9 C C1' CTP . . . F 5 -6.711 10.766 -8.228 1 65.21 ? C1' CTP 305 A 1 HETATM 10 C C2' CTP . . . F 5 -5.545 10.125 -9.013 1 68.56 ? C2' CTP 305 A 1 HETATM 11 O O2' CTP . . . F 5 -5.983 9.176 -9.99 1 74.47 ? O2' CTP 305 A 1 HETATM 12 C C3' CTP . . . F 5 -4.63 9.453 -8.001 1 66.83 ? C3' CTP 305 A 1 HETATM 13 C C4' CTP . . . F 5 -5.259 9.737 -6.631 1 64.11 ? C4' CTP 305 A 1 HETATM 14 O O4' CTP . . . F 5 -6.361 10.647 -6.831 1 67.02 ? O4' CTP 305 A 1 HETATM 15 O O3' CTP . . . F 5 -4.476 8.055 -8.268 1 65.85 ? O3' CTP 305 A 1 HETATM 16 C C5' CTP . . . F 5 -4.242 10.399 -5.695 1 59.85 ? C5' CTP 305 A 1 HETATM 17 O O5' CTP . . . F 5 -3.929 11.692 -6.238 1 51.22 ? O5' CTP 305 A 1 HETATM 18 P PA CTP . . . F 5 -2.427 12.227 -6.634 1 51.38 ? PA CTP 305 A 1 HETATM 19 O O1A CTP . . . F 5 -1.55 11.247 -7.436 1 46.46 ? O1A CTP 305 A 1 HETATM 20 O O2A CTP . . . F 5 -2.72 13.604 -7.24 1 30.7 ? O2A CTP 305 A 1 HETATM 21 O O3A CTP . . . F 5 -1.764 12.446 -5.121 1 50.63 ? O3A CTP 305 A 1 HETATM 22 P PB CTP . . . F 5 -0.88 11.473 -4.116 1 48.32 ? PB CTP 305 A 1 HETATM 23 O O1B CTP . . . F 5 -0.929 9.99 -4.553 1 45.52 ? O1B CTP 305 A 1 HETATM 24 O O2B CTP . . . F 5 -1.246 11.887 -2.696 1 46.29 ? O2B CTP 305 A 1 HETATM 25 O O3B CTP . . . F 5 0.622 12.092 -4.202 1 41.97 ? O3B CTP 305 A 1 HETATM 26 P PG CTP . . . F 5 1.879 11.558 -5.11 1 40.09 ? PG CTP 305 A 1 HETATM 27 O O1G CTP . . . F 5 1.215 11.02 -6.384 1 39.21 ? O1G CTP 305 A 1 HETATM 28 O O2G CTP . . . F 5 2.593 10.525 -4.227 1 44.77 ? O2G CTP 305 A 1 HETATM 29 O O3G CTP . . . F 5 2.733 12.791 -5.355 1 35.89 ? O3G CTP 305 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #