data_8YSG # _model_server_result.job_id dEQIGg5x1FtYwsfNMMmIBQ _model_server_result.datetime_utc '2025-02-05 01:38:18' _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 8ysg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 8YSG # _exptl.entry_id 8YSG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.621 _cell.angle_gamma 90 _cell.entry_id 8YSG _cell.length_a 35.033 _cell.length_b 100.404 _cell.length_c 46.398 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 x,y,z _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 ? 2 B N N ? 2 C N 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 metalc ? metalc1 A OD2 ASP 78 A ASP 78 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 A OD1 ASP 78 A ASP 78 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A OD2 ASP 78 A ASP 78 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc4 A OD1 ASP 80 A ASP 80 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc5 A OD2 ASP 80 A ASP 80 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc6 A OD2 ASP 129 A ASP 129 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc7 B O2G GTP . A GTP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc8 B O2B GTP . A GTP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc9 B O1A GTP . A GTP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc10 B O1A GTP . A GTP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc11 C O3' GTP . A GTP 402 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc12 C O2' GTP . A GTP 402 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc13 D MG MG . A MG 403 1_555 F O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 GTP doub 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 8YSG _atom_sites.fract_transf_matrix[1][1] 0.028545 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00587 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00996 _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] 0.022004 _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 GTP A 1 401 360 GTP GTP . C 2 GTP A 1 402 361 GTP GTP . D 3 MG A 1 403 380 MG MG . E 3 MG A 1 404 381 MG MG . F 4 HOH A 1 501 441 HOH HOH . F 4 HOH A 2 502 449 HOH HOH . F 4 HOH A 3 503 500 HOH HOH . F 4 HOH A 4 504 403 HOH HOH . F 4 HOH A 5 505 506 HOH HOH . F 4 HOH A 6 506 413 HOH HOH . F 4 HOH A 7 507 482 HOH HOH . F 4 HOH A 8 508 425 HOH HOH . F 4 HOH A 9 509 444 HOH HOH . F 4 HOH A 10 510 400 HOH HOH . F 4 HOH A 11 511 499 HOH HOH . F 4 HOH A 12 512 467 HOH HOH . F 4 HOH A 13 513 428 HOH HOH . F 4 HOH A 14 514 510 HOH HOH . F 4 HOH A 15 515 420 HOH HOH . F 4 HOH A 16 516 501 HOH HOH . F 4 HOH A 17 517 445 HOH HOH . F 4 HOH A 18 518 494 HOH HOH . F 4 HOH A 19 519 419 HOH HOH . F 4 HOH A 20 520 405 HOH HOH . F 4 HOH A 21 521 414 HOH HOH . F 4 HOH A 22 522 447 HOH HOH . F 4 HOH A 23 523 440 HOH HOH . F 4 HOH A 24 524 463 HOH HOH . F 4 HOH A 25 525 442 HOH HOH . F 4 HOH A 26 526 483 HOH HOH . F 4 HOH A 27 527 408 HOH HOH . F 4 HOH A 28 528 429 HOH HOH . F 4 HOH A 29 529 422 HOH HOH . F 4 HOH A 30 530 416 HOH HOH . F 4 HOH A 31 531 439 HOH HOH . F 4 HOH A 32 532 460 HOH HOH . F 4 HOH A 33 533 410 HOH HOH . F 4 HOH A 34 534 404 HOH HOH . F 4 HOH A 35 535 437 HOH HOH . F 4 HOH A 36 536 451 HOH HOH . F 4 HOH A 37 537 435 HOH HOH . F 4 HOH A 38 538 450 HOH HOH . F 4 HOH A 39 539 479 HOH HOH . F 4 HOH A 40 540 457 HOH HOH . F 4 HOH A 41 541 433 HOH HOH . F 4 HOH A 42 542 423 HOH HOH . F 4 HOH A 43 543 407 HOH HOH . F 4 HOH A 44 544 491 HOH HOH . F 4 HOH A 45 545 459 HOH HOH . F 4 HOH A 46 546 503 HOH HOH . F 4 HOH A 47 547 432 HOH HOH . F 4 HOH A 48 548 495 HOH HOH . F 4 HOH A 49 549 402 HOH HOH . F 4 HOH A 50 550 421 HOH HOH . F 4 HOH A 51 551 412 HOH HOH . F 4 HOH A 52 552 417 HOH HOH . F 4 HOH A 53 553 446 HOH HOH . F 4 HOH A 54 554 448 HOH HOH . F 4 HOH A 55 555 431 HOH HOH . F 4 HOH A 56 556 456 HOH HOH . F 4 HOH A 57 557 474 HOH HOH . F 4 HOH A 58 558 438 HOH HOH . F 4 HOH A 59 559 461 HOH HOH . F 4 HOH A 60 560 462 HOH HOH . F 4 HOH A 61 561 458 HOH HOH . F 4 HOH A 62 562 443 HOH HOH . F 4 HOH A 63 563 415 HOH HOH . F 4 HOH A 64 564 426 HOH HOH . F 4 HOH A 65 565 454 HOH HOH . F 4 HOH A 66 566 427 HOH HOH . F 4 HOH A 67 567 453 HOH HOH . F 4 HOH A 68 568 473 HOH HOH . F 4 HOH A 69 569 434 HOH HOH . F 4 HOH A 70 570 418 HOH HOH . F 4 HOH A 71 571 411 HOH HOH . F 4 HOH A 72 572 406 HOH HOH . F 4 HOH A 73 573 493 HOH HOH . F 4 HOH A 74 574 401 HOH HOH . F 4 HOH A 75 575 504 HOH HOH . F 4 HOH A 76 576 455 HOH HOH . F 4 HOH A 77 577 488 HOH HOH . F 4 HOH A 78 578 464 HOH HOH . F 4 HOH A 79 579 409 HOH HOH . F 4 HOH A 80 580 452 HOH HOH . F 4 HOH A 81 581 485 HOH HOH . F 4 HOH A 82 582 487 HOH HOH . F 4 HOH A 83 583 436 HOH HOH . F 4 HOH A 84 584 424 HOH HOH . F 4 HOH A 85 585 492 HOH HOH . F 4 HOH A 86 586 465 HOH HOH . F 4 HOH A 87 587 509 HOH HOH . F 4 HOH A 88 588 475 HOH HOH . F 4 HOH A 89 589 430 HOH HOH . F 4 HOH A 90 590 472 HOH HOH . F 4 HOH A 91 591 470 HOH HOH . F 4 HOH A 92 592 490 HOH HOH . F 4 HOH A 93 593 478 HOH HOH . F 4 HOH A 94 594 486 HOH HOH . F 4 HOH A 95 595 505 HOH HOH . F 4 HOH A 96 596 466 HOH HOH . F 4 HOH A 97 597 480 HOH HOH . F 4 HOH A 98 598 468 HOH HOH . F 4 HOH A 99 599 481 HOH HOH . F 4 HOH A 100 600 498 HOH HOH . F 4 HOH A 101 601 476 HOH HOH . F 4 HOH A 102 602 502 HOH HOH . F 4 HOH A 103 603 477 HOH HOH . F 4 HOH A 104 604 496 HOH HOH . F 4 HOH A 105 605 469 HOH HOH . F 4 HOH A 106 606 471 HOH HOH . F 4 HOH A 107 607 489 HOH HOH . F 4 HOH A 108 608 507 HOH HOH . F 4 HOH A 109 609 484 HOH HOH . F 4 HOH A 110 610 497 HOH HOH . F 4 HOH A 111 611 508 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 GTP . . . C 2 18.306 8.909 -2.151 1 106.73 ? PG GTP 402 A 1 HETATM 2 O O1G GTP . . . C 2 17.827 7.674 -2.881 1 98.97 ? O1G GTP 402 A 1 HETATM 3 O O2G GTP . . . C 2 18.192 10.153 -2.996 1 109.04 ? O2G GTP 402 A 1 HETATM 4 O O3G GTP . . . C 2 19.687 8.737 -1.56 1 107.45 ? O3G GTP 402 A 1 HETATM 5 O O3B GTP . . . C 2 17.305 9.124 -0.876 1 106.33 ? O3B GTP 402 A 1 HETATM 6 P PB GTP . . . C 2 17.298 10.109 0.396 1 101.46 ? PB GTP 402 A 1 HETATM 7 O O1B GTP . . . C 2 18.679 10.149 0.971 1 101.84 ? O1B GTP 402 A 1 HETATM 8 O O2B GTP . . . C 2 16.652 11.389 -0.019 1 101.43 ? O2B GTP 402 A 1 HETATM 9 O O3A GTP . . . C 2 16.332 9.348 1.438 1 94.32 ? O3A GTP 402 A 1 HETATM 10 P PA GTP . . . C 2 14.984 8.458 1.37 1 91.23 ? PA GTP 402 A 1 HETATM 11 O O1A GTP . . . C 2 13.806 9.36 1.214 1 75.93 ? O1A GTP 402 A 1 HETATM 12 O O2A GTP . . . C 2 15.152 7.375 0.356 1 94.94 ? O2A GTP 402 A 1 HETATM 13 O O5' GTP . . . C 2 14.956 7.798 2.838 1 91.46 ? O5' GTP 402 A 1 HETATM 14 C C5' GTP . . . C 2 14.666 8.607 4.01 1 83.07 ? C5' GTP 402 A 1 HETATM 15 C C4' GTP . . . C 2 13.369 8.154 4.64 1 79.75 ? C4' GTP 402 A 1 HETATM 16 O O4' GTP . . . C 2 12.28 8.402 3.722 1 79.19 ? O4' GTP 402 A 1 HETATM 17 C C3' GTP . . . C 2 13.262 6.665 4.978 1 78.32 ? C3' GTP 402 A 1 HETATM 18 O O3' GTP . . . C 2 13.781 6.435 6.284 1 67.84 ? O3' GTP 402 A 1 HETATM 19 C C2' GTP . . . C 2 11.752 6.395 4.887 1 77.25 ? C2' GTP 402 A 1 HETATM 20 O O2' GTP . . . C 2 11.123 6.555 6.14 1 71.89 ? O2' GTP 402 A 1 HETATM 21 C C1' GTP . . . C 2 11.251 7.45 3.895 1 79.22 ? C1' GTP 402 A 1 HETATM 22 N N9 GTP . . . C 2 10.901 6.946 2.568 1 79.86 ? N9 GTP 402 A 1 HETATM 23 C C8 GTP . . . C 2 11.779 6.549 1.587 1 79.75 ? C8 GTP 402 A 1 HETATM 24 N N7 GTP . . . C 2 11.194 6.207 0.465 1 71.99 ? N7 GTP 402 A 1 HETATM 25 C C5 GTP . . . C 2 9.841 6.399 0.716 1 72.28 ? C5 GTP 402 A 1 HETATM 26 C C6 GTP . . . C 2 8.722 6.195 -0.133 1 70.82 ? C6 GTP 402 A 1 HETATM 27 O O6 GTP . . . C 2 8.708 5.807 -1.31 1 68.25 ? O6 GTP 402 A 1 HETATM 28 N N1 GTP . . . C 2 7.528 6.504 0.52 1 70.59 ? N1 GTP 402 A 1 HETATM 29 C C2 GTP . . . C 2 7.421 6.963 1.812 1 67.52 ? C2 GTP 402 A 1 HETATM 30 N N2 GTP . . . C 2 6.179 7.198 2.257 1 71.69 ? N2 GTP 402 A 1 HETATM 31 N N3 GTP . . . C 2 8.47 7.17 2.613 1 68.84 ? N3 GTP 402 A 1 HETATM 32 C C4 GTP . . . C 2 9.645 6.862 2.004 1 74.47 ? C4 GTP 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #