data_1CG4 # _model_server_result.job_id GgBA3u7Y2HPPmp30GMcIgw _model_server_result.datetime_utc '2025-02-05 15:48:40' _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 1cg4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":432}' # _entry.id 1CG4 # _exptl.entry_id 1CG4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 1CG4 _cell.length_a 80.21 _cell.length_b 80.21 _cell.length_c 157.87 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CG4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866214 0 -0.865837 0.5 0 0 0 -1 0 0 105.652404 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASP 13 A ASP 13 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc2 A O GLY 40 A GLY 40 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc3 D O2B GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc4 D O2A GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 B MG MG . A MG 435 1_555 C O1 IMO . A IMO 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc6 B MG MG . A MG 435 1_555 E O HOH . A HOH 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1CG4 _atom_sites.fract_transf_matrix[1][1] 0.01252 _atom_sites.fract_transf_matrix[1][2] 0.00723 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01446 _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] 0.00631 _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 MG A 1 435 435 MG MG . C 3 IMO A 1 440 440 IMO IPP . D 4 GDP A 1 432 432 GDP GDP . E 5 HOH A 1 441 1 HOH HOH . E 5 HOH A 2 442 3 HOH HOH . E 5 HOH A 3 443 4 HOH HOH . E 5 HOH A 4 444 5 HOH HOH . E 5 HOH A 5 445 6 HOH HOH . E 5 HOH A 6 446 7 HOH HOH . E 5 HOH A 7 447 8 HOH HOH . E 5 HOH A 8 448 9 HOH HOH . E 5 HOH A 9 449 10 HOH HOH . E 5 HOH A 10 450 11 HOH HOH . E 5 HOH A 11 451 12 HOH HOH . E 5 HOH A 12 452 13 HOH HOH . E 5 HOH A 13 453 14 HOH HOH . E 5 HOH A 14 454 15 HOH HOH . E 5 HOH A 15 455 16 HOH HOH . E 5 HOH A 16 456 17 HOH HOH . E 5 HOH A 17 457 18 HOH HOH . E 5 HOH A 18 458 19 HOH HOH . E 5 HOH A 19 459 20 HOH HOH . E 5 HOH A 20 460 21 HOH HOH . E 5 HOH A 21 461 22 HOH HOH . E 5 HOH A 22 462 23 HOH HOH . E 5 HOH A 23 463 24 HOH HOH . E 5 HOH A 24 464 25 HOH HOH . E 5 HOH A 25 465 26 HOH HOH . E 5 HOH A 26 466 27 HOH HOH . E 5 HOH A 27 467 28 HOH HOH . E 5 HOH A 28 468 29 HOH HOH . E 5 HOH A 29 469 30 HOH HOH . E 5 HOH A 30 470 31 HOH HOH . E 5 HOH A 31 471 32 HOH HOH . E 5 HOH A 32 472 33 HOH HOH . E 5 HOH A 33 473 34 HOH HOH . E 5 HOH A 34 474 35 HOH HOH . E 5 HOH A 35 475 36 HOH HOH . E 5 HOH A 36 476 37 HOH HOH . E 5 HOH A 37 477 38 HOH HOH . E 5 HOH A 38 478 39 HOH HOH . E 5 HOH A 39 479 40 HOH HOH . E 5 HOH A 40 480 41 HOH HOH . E 5 HOH A 41 481 42 HOH HOH . E 5 HOH A 42 482 43 HOH HOH . E 5 HOH A 43 483 44 HOH HOH . E 5 HOH A 44 484 45 HOH HOH . E 5 HOH A 45 485 46 HOH HOH . E 5 HOH A 46 486 47 HOH HOH . E 5 HOH A 47 487 48 HOH HOH . E 5 HOH A 48 488 50 HOH HOH . E 5 HOH A 49 489 51 HOH HOH . E 5 HOH A 50 490 52 HOH HOH . E 5 HOH A 51 491 53 HOH HOH . E 5 HOH A 52 492 54 HOH HOH . E 5 HOH A 53 493 55 HOH HOH . E 5 HOH A 54 494 56 HOH HOH . E 5 HOH A 55 495 57 HOH HOH . E 5 HOH A 56 496 58 HOH HOH . E 5 HOH A 57 497 59 HOH HOH . E 5 HOH A 58 498 60 HOH HOH . E 5 HOH A 59 499 61 HOH HOH . E 5 HOH A 60 500 62 HOH HOH . E 5 HOH A 61 501 63 HOH HOH . E 5 HOH A 62 502 64 HOH HOH . E 5 HOH A 63 503 65 HOH HOH . E 5 HOH A 64 504 67 HOH HOH . E 5 HOH A 65 505 68 HOH HOH . E 5 HOH A 66 506 69 HOH HOH . E 5 HOH A 67 507 71 HOH HOH . E 5 HOH A 68 508 72 HOH HOH . E 5 HOH A 69 509 73 HOH HOH . E 5 HOH A 70 510 74 HOH HOH . E 5 HOH A 71 511 76 HOH HOH . E 5 HOH A 72 512 77 HOH HOH . E 5 HOH A 73 513 78 HOH HOH . E 5 HOH A 74 514 79 HOH HOH . E 5 HOH A 75 515 80 HOH HOH . E 5 HOH A 76 516 81 HOH HOH . E 5 HOH A 77 517 82 HOH HOH . E 5 HOH A 78 518 83 HOH HOH . E 5 HOH A 79 519 84 HOH HOH . E 5 HOH A 80 520 85 HOH HOH . E 5 HOH A 81 521 86 HOH HOH . E 5 HOH A 82 522 87 HOH HOH . E 5 HOH A 83 523 88 HOH HOH . E 5 HOH A 84 524 89 HOH HOH . E 5 HOH A 85 525 90 HOH HOH . E 5 HOH A 86 526 91 HOH HOH . E 5 HOH A 87 527 92 HOH HOH . E 5 HOH A 88 528 93 HOH HOH . E 5 HOH A 89 529 94 HOH HOH . E 5 HOH A 90 530 95 HOH HOH . E 5 HOH A 91 531 96 HOH HOH . E 5 HOH A 92 532 97 HOH HOH . E 5 HOH A 93 533 99 HOH HOH . E 5 HOH A 94 534 100 HOH HOH . E 5 HOH A 95 535 101 HOH HOH . E 5 HOH A 96 536 102 HOH HOH . E 5 HOH A 97 537 103 HOH HOH . E 5 HOH A 98 538 104 HOH HOH . E 5 HOH A 99 539 105 HOH HOH . E 5 HOH A 100 540 106 HOH HOH . E 5 HOH A 101 541 107 HOH HOH . E 5 HOH A 102 542 108 HOH HOH . E 5 HOH A 103 543 109 HOH HOH . E 5 HOH A 104 544 110 HOH HOH . E 5 HOH A 105 545 111 HOH HOH . E 5 HOH A 106 546 112 HOH HOH . E 5 HOH A 107 547 113 HOH HOH . E 5 HOH A 108 548 114 HOH HOH . E 5 HOH A 109 549 115 HOH HOH . E 5 HOH A 110 550 116 HOH HOH . E 5 HOH A 111 551 117 HOH HOH . E 5 HOH A 112 552 118 HOH HOH . E 5 HOH A 113 553 119 HOH HOH . E 5 HOH A 114 554 120 HOH HOH . E 5 HOH A 115 555 121 HOH HOH . E 5 HOH A 116 556 122 HOH HOH . E 5 HOH A 117 557 123 HOH HOH . E 5 HOH A 118 558 124 HOH HOH . E 5 HOH A 119 559 125 HOH HOH . E 5 HOH A 120 560 126 HOH HOH . E 5 HOH A 121 561 127 HOH HOH . E 5 HOH A 122 562 128 HOH HOH . E 5 HOH A 123 563 129 HOH HOH . E 5 HOH A 124 564 130 HOH HOH . E 5 HOH A 125 565 131 HOH HOH . E 5 HOH A 126 566 132 HOH HOH . E 5 HOH A 127 567 133 HOH HOH . E 5 HOH A 128 568 134 HOH HOH . E 5 HOH A 129 569 135 HOH HOH . E 5 HOH A 130 570 136 HOH HOH . E 5 HOH A 131 571 137 HOH HOH . E 5 HOH A 132 572 138 HOH HOH . E 5 HOH A 133 573 139 HOH HOH . E 5 HOH A 134 574 141 HOH HOH . E 5 HOH A 135 575 142 HOH HOH . E 5 HOH A 136 576 143 HOH HOH . E 5 HOH A 137 577 144 HOH HOH . E 5 HOH A 138 578 145 HOH HOH . E 5 HOH A 139 579 146 HOH HOH . E 5 HOH A 140 580 147 HOH HOH . E 5 HOH A 141 581 148 HOH HOH . E 5 HOH A 142 582 149 HOH HOH . E 5 HOH A 143 583 150 HOH HOH . E 5 HOH A 144 584 151 HOH HOH . E 5 HOH A 145 585 152 HOH HOH . E 5 HOH A 146 586 153 HOH HOH . E 5 HOH A 147 587 154 HOH HOH . E 5 HOH A 148 588 155 HOH HOH . E 5 HOH A 149 589 156 HOH HOH . E 5 HOH A 150 590 157 HOH HOH . E 5 HOH A 151 591 158 HOH HOH . E 5 HOH A 152 592 159 HOH HOH . E 5 HOH A 153 593 160 HOH HOH . E 5 HOH A 154 594 161 HOH HOH . E 5 HOH A 155 595 162 HOH HOH . E 5 HOH A 156 596 163 HOH HOH . E 5 HOH A 157 597 164 HOH HOH . E 5 HOH A 158 598 166 HOH HOH . E 5 HOH A 159 599 167 HOH HOH . E 5 HOH A 160 600 168 HOH HOH . E 5 HOH A 161 601 169 HOH HOH . E 5 HOH A 162 602 170 HOH HOH . E 5 HOH A 163 603 171 HOH HOH . E 5 HOH A 164 604 172 HOH HOH . E 5 HOH A 165 605 173 HOH HOH . E 5 HOH A 166 606 174 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 PB GDP . . . D 4 -4.637 47.37 44.711 1 25.06 ? PB GDP 432 A 1 HETATM 2 O O1B GDP . . . D 4 -4.964 46.664 43.426 1 27.56 ? O1B GDP 432 A 1 HETATM 3 O O2B GDP . . . D 4 -5.549 48.482 44.903 1 19.16 ? O2B GDP 432 A 1 HETATM 4 O O3B GDP . . . D 4 -4.564 46.413 45.848 1 24.27 ? O3B GDP 432 A 1 HETATM 5 O O3A GDP . . . D 4 -3.16 47.965 44.665 1 29.1 ? O3A GDP 432 A 1 HETATM 6 P PA GDP . . . D 4 -2.936 49.404 43.962 1 26.5 ? PA GDP 432 A 1 HETATM 7 O O1A GDP . . . D 4 -2.58 49.185 42.542 1 25.74 ? O1A GDP 432 A 1 HETATM 8 O O2A GDP . . . D 4 -3.955 50.488 44.24 1 22.79 ? O2A GDP 432 A 1 HETATM 9 O O5' GDP . . . D 4 -1.59 49.766 44.764 1 22.96 ? O5' GDP 432 A 1 HETATM 10 C C5' GDP . . . D 4 -0.497 48.886 44.515 1 25.21 ? C5' GDP 432 A 1 HETATM 11 C C4' GDP . . . D 4 0.552 49.774 43.953 1 27.14 ? C4' GDP 432 A 1 HETATM 12 O O4' GDP . . . D 4 1.885 49.469 44.188 1 25.65 ? O4' GDP 432 A 1 HETATM 13 C C3' GDP . . . D 4 0.554 50.011 42.499 1 27.67 ? C3' GDP 432 A 1 HETATM 14 O O3' GDP . . . D 4 1.28 51.272 42.274 1 27.09 ? O3' GDP 432 A 1 HETATM 15 C C2' GDP . . . D 4 1.513 48.902 41.967 1 29.22 ? C2' GDP 432 A 1 HETATM 16 O O2' GDP . . . D 4 2.022 49.443 40.732 1 33.76 ? O2' GDP 432 A 1 HETATM 17 C C1' GDP . . . D 4 2.551 48.89 43.013 1 26.32 ? C1' GDP 432 A 1 HETATM 18 N N9 GDP . . . D 4 3.117 47.646 43.326 1 27.41 ? N9 GDP 432 A 1 HETATM 19 C C8 GDP . . . D 4 2.572 46.369 43.42 1 27.26 ? C8 GDP 432 A 1 HETATM 20 N N7 GDP . . . D 4 3.414 45.464 43.967 1 27.74 ? N7 GDP 432 A 1 HETATM 21 C C5 GDP . . . D 4 4.559 46.203 44.247 1 20.7 ? C5 GDP 432 A 1 HETATM 22 C C6 GDP . . . D 4 5.735 45.767 44.819 1 24.52 ? C6 GDP 432 A 1 HETATM 23 O O6 GDP . . . D 4 5.996 44.607 45.203 1 18.82 ? O6 GDP 432 A 1 HETATM 24 N N1 GDP . . . D 4 6.652 46.823 44.904 1 19.06 ? N1 GDP 432 A 1 HETATM 25 C C2 GDP . . . D 4 6.437 48.127 44.496 1 23.09 ? C2 GDP 432 A 1 HETATM 26 N N2 GDP . . . D 4 7.393 49.05 44.668 1 22.5 ? N2 GDP 432 A 1 HETATM 27 N N3 GDP . . . D 4 5.29 48.511 43.956 1 22.37 ? N3 GDP 432 A 1 HETATM 28 C C4 GDP . . . D 4 4.422 47.502 43.866 1 22.77 ? C4 GDP 432 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 361 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #