data_5KY9 # _model_server_result.job_id NymHSfxva9k4X8KPDgH8Mw _model_server_result.datetime_utc '2024-10-12 08:25:25' _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 5ky9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5KY9 # _exptl.entry_id 5KY9 _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 90 _cell.entry_id 5KY9 _cell.length_a 52.1 _cell.length_b 66.52 _cell.length_c 109.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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,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 # _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 disulf ? disulf1 A SG CYS 14 A CYS 43 1_555 A SG CYS 16 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 102 A CYS 131 1_555 A SG CYS 116 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 A SG CYS 225 A CYS 254 1_555 A SG CYS 259 A CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf4 A SG CYS 243 A CYS 272 1_555 A SG CYS 330 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 B SG CYS 5 B CYS 456 1_555 B SG CYS 16 B CYS 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 10 B CYS 461 1_555 B SG CYS 25 B CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 B SG CYS 27 B CYS 478 1_555 B SG CYS 36 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 38 A ASN 67 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 ? # _atom_sites.entry_id 5KY9 _atom_sites.fract_transf_matrix[1][1] 0.019194 _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] 0.015033 _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] 0.009094 _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 C 3 NAG A 1 401 401 NAG NAG . D 4 GDP A 1 402 1 GDP GDP . E 5 HOH A 1 501 149 HOH HOH . E 5 HOH A 2 502 94 HOH HOH . E 5 HOH A 3 503 17 HOH HOH . E 5 HOH A 4 504 152 HOH HOH . E 5 HOH A 5 505 57 HOH HOH . E 5 HOH A 6 506 110 HOH HOH . E 5 HOH A 7 507 54 HOH HOH . E 5 HOH A 8 508 9 HOH HOH . E 5 HOH A 9 509 97 HOH HOH . E 5 HOH A 10 510 58 HOH HOH . E 5 HOH A 11 511 103 HOH HOH . E 5 HOH A 12 512 68 HOH HOH . E 5 HOH A 13 513 120 HOH HOH . E 5 HOH A 14 514 40 HOH HOH . E 5 HOH A 15 515 77 HOH HOH . E 5 HOH A 16 516 21 HOH HOH . E 5 HOH A 17 517 61 HOH HOH . E 5 HOH A 18 518 4 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 34 HOH HOH . E 5 HOH A 21 521 13 HOH HOH . E 5 HOH A 22 522 99 HOH HOH . E 5 HOH A 23 523 30 HOH HOH . E 5 HOH A 24 524 23 HOH HOH . E 5 HOH A 25 525 37 HOH HOH . E 5 HOH A 26 526 113 HOH HOH . E 5 HOH A 27 527 3 HOH HOH . E 5 HOH A 28 528 24 HOH HOH . E 5 HOH A 29 529 55 HOH HOH . E 5 HOH A 30 530 16 HOH HOH . E 5 HOH A 31 531 90 HOH HOH . E 5 HOH A 32 532 111 HOH HOH . E 5 HOH A 33 533 35 HOH HOH . E 5 HOH A 34 534 31 HOH HOH . E 5 HOH A 35 535 115 HOH HOH . E 5 HOH A 36 536 80 HOH HOH . E 5 HOH A 37 537 8 HOH HOH . E 5 HOH A 38 538 49 HOH HOH . E 5 HOH A 39 539 109 HOH HOH . E 5 HOH A 40 540 81 HOH HOH . E 5 HOH A 41 541 1 HOH HOH . E 5 HOH A 42 542 12 HOH HOH . E 5 HOH A 43 543 28 HOH HOH . E 5 HOH A 44 544 5 HOH HOH . E 5 HOH A 45 545 67 HOH HOH . E 5 HOH A 46 546 117 HOH HOH . E 5 HOH A 47 547 27 HOH HOH . E 5 HOH A 48 548 29 HOH HOH . E 5 HOH A 49 549 107 HOH HOH . E 5 HOH A 50 550 104 HOH HOH . E 5 HOH A 51 551 10 HOH HOH . E 5 HOH A 52 552 79 HOH HOH . E 5 HOH A 53 553 133 HOH HOH . E 5 HOH A 54 554 132 HOH HOH . E 5 HOH A 55 555 39 HOH HOH . E 5 HOH A 56 556 14 HOH HOH . E 5 HOH A 57 557 52 HOH HOH . E 5 HOH A 58 558 20 HOH HOH . E 5 HOH A 59 559 114 HOH HOH . E 5 HOH A 60 560 129 HOH HOH . E 5 HOH A 61 561 83 HOH HOH . E 5 HOH A 62 562 139 HOH HOH . E 5 HOH A 63 563 123 HOH HOH . E 5 HOH A 64 564 15 HOH HOH . E 5 HOH A 65 565 64 HOH HOH . E 5 HOH A 66 566 140 HOH HOH . E 5 HOH A 67 567 18 HOH HOH . E 5 HOH A 68 568 72 HOH HOH . E 5 HOH A 69 569 101 HOH HOH . E 5 HOH A 70 570 46 HOH HOH . E 5 HOH A 71 571 73 HOH HOH . E 5 HOH A 72 572 22 HOH HOH . E 5 HOH A 73 573 91 HOH HOH . E 5 HOH A 74 574 142 HOH HOH . E 5 HOH A 75 575 51 HOH HOH . E 5 HOH A 76 576 25 HOH HOH . E 5 HOH A 77 577 147 HOH HOH . E 5 HOH A 78 578 50 HOH HOH . E 5 HOH A 79 579 125 HOH HOH . E 5 HOH A 80 580 89 HOH HOH . E 5 HOH A 81 581 122 HOH HOH . E 5 HOH A 82 582 6 HOH HOH . E 5 HOH A 83 583 11 HOH HOH . E 5 HOH A 84 584 70 HOH HOH . E 5 HOH A 85 585 116 HOH HOH . E 5 HOH A 86 586 2 HOH HOH . E 5 HOH A 87 587 42 HOH HOH . E 5 HOH A 88 588 71 HOH HOH . E 5 HOH A 89 589 135 HOH HOH . E 5 HOH A 90 590 119 HOH HOH . E 5 HOH A 91 591 45 HOH HOH . E 5 HOH A 92 592 82 HOH HOH . E 5 HOH A 93 593 86 HOH HOH . E 5 HOH A 94 594 7 HOH HOH . E 5 HOH A 95 595 41 HOH HOH . E 5 HOH A 96 596 48 HOH HOH . E 5 HOH A 97 597 69 HOH HOH . E 5 HOH A 98 598 102 HOH HOH . E 5 HOH A 99 599 143 HOH HOH . E 5 HOH A 100 600 38 HOH HOH . E 5 HOH A 101 601 63 HOH HOH . E 5 HOH A 102 602 106 HOH HOH . E 5 HOH A 103 603 47 HOH HOH . E 5 HOH A 104 604 128 HOH HOH . E 5 HOH A 105 605 87 HOH HOH . E 5 HOH A 106 606 108 HOH HOH . E 5 HOH A 107 607 33 HOH HOH . E 5 HOH A 108 608 75 HOH HOH . E 5 HOH A 109 609 153 HOH HOH . E 5 HOH A 110 610 92 HOH HOH . E 5 HOH A 111 611 76 HOH HOH . E 5 HOH A 112 612 32 HOH HOH . E 5 HOH A 113 613 148 HOH HOH . E 5 HOH A 114 614 85 HOH HOH . E 5 HOH A 115 615 105 HOH HOH . E 5 HOH A 116 616 60 HOH HOH . E 5 HOH A 117 617 74 HOH HOH . E 5 HOH A 118 618 93 HOH HOH . E 5 HOH A 119 619 62 HOH HOH . E 5 HOH A 120 620 66 HOH HOH . E 5 HOH A 121 621 65 HOH HOH . E 5 HOH A 122 622 26 HOH HOH . E 5 HOH A 123 623 146 HOH HOH . E 5 HOH A 124 624 126 HOH HOH . E 5 HOH A 125 625 88 HOH HOH . E 5 HOH A 126 626 78 HOH HOH . E 5 HOH A 127 627 56 HOH HOH . E 5 HOH A 128 628 36 HOH HOH . E 5 HOH A 129 629 130 HOH HOH . E 5 HOH A 130 630 95 HOH HOH . E 5 HOH A 131 631 136 HOH HOH . E 5 HOH A 132 632 131 HOH HOH . E 5 HOH A 133 633 145 HOH HOH . E 5 HOH A 134 634 100 HOH HOH . E 5 HOH A 135 635 43 HOH HOH . E 5 HOH A 136 636 84 HOH HOH . E 5 HOH A 137 637 134 HOH HOH . E 5 HOH A 138 638 144 HOH HOH . E 5 HOH A 139 639 127 HOH HOH . E 5 HOH A 140 640 151 HOH HOH . E 5 HOH A 141 641 138 HOH HOH . E 5 HOH A 142 642 124 HOH HOH . E 5 HOH A 143 643 59 HOH HOH . E 5 HOH A 144 644 112 HOH HOH . E 5 HOH A 145 645 150 HOH HOH . E 5 HOH A 146 646 98 HOH HOH . E 5 HOH A 147 647 44 HOH HOH . E 5 HOH A 148 648 53 HOH HOH . F 5 HOH B 1 501 121 HOH HOH . F 5 HOH B 2 502 118 HOH HOH . F 5 HOH B 3 503 96 HOH HOH . F 5 HOH B 4 504 141 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 14.123 31.202 5.799 1 47.86 ? PB GDP 402 A 1 HETATM 2 O O1B GDP . . . D 4 15.436 31.925 5.848 1 45.41 ? O1B GDP 402 A 1 HETATM 3 O O2B GDP . . . D 4 14.178 29.829 5.201 1 50.71 ? O2B GDP 402 A 1 HETATM 4 O O3B GDP . . . D 4 12.998 32.047 5.281 1 48.22 ? O3B GDP 402 A 1 HETATM 5 O O3A GDP . . . D 4 13.828 30.893 7.34 1 56.37 ? O3A GDP 402 A 1 HETATM 6 P PA GDP . . . D 4 12.544 31.408 8.146 1 64.67 ? PA GDP 402 A 1 HETATM 7 O O1A GDP . . . D 4 12.263 30.421 9.244 1 61.96 ? O1A GDP 402 A 1 HETATM 8 O O2A GDP . . . D 4 12.718 32.868 8.467 1 68.54 ? O2A GDP 402 A 1 HETATM 9 O O5' GDP . . . D 4 11.365 31.264 7.076 1 72.63 ? O5' GDP 402 A 1 HETATM 10 C C5' GDP . . . D 4 11.006 29.973 6.609 1 72.99 ? C5' GDP 402 A 1 HETATM 11 C C4' GDP . . . D 4 9.664 29.622 7.221 1 71.34 ? C4' GDP 402 A 1 HETATM 12 O O4' GDP . . . D 4 8.961 28.711 6.371 1 69.08 ? O4' GDP 402 A 1 HETATM 13 C C3' GDP . . . D 4 9.808 28.946 8.573 1 68.43 ? C3' GDP 402 A 1 HETATM 14 O O3' GDP . . . D 4 9.724 29.859 9.664 1 66.69 ? O3' GDP 402 A 1 HETATM 15 C C2' GDP . . . D 4 8.668 27.957 8.583 1 67.62 ? C2' GDP 402 A 1 HETATM 16 O O2' GDP . . . D 4 7.472 28.563 9.07 1 64.24 ? O2' GDP 402 A 1 HETATM 17 C C1' GDP . . . D 4 8.538 27.577 7.123 1 65.23 ? C1' GDP 402 A 1 HETATM 18 N N9 GDP . . . D 4 9.449 26.439 6.886 1 56.3 ? N9 GDP 402 A 1 HETATM 19 C C8 GDP . . . D 4 10.55 26.454 6.117 1 52.78 ? C8 GDP 402 A 1 HETATM 20 N N7 GDP . . . D 4 11.156 25.247 6.134 1 46.21 ? N7 GDP 402 A 1 HETATM 21 C C5 GDP . . . D 4 10.44 24.443 6.931 1 49.89 ? C5 GDP 402 A 1 HETATM 22 C C6 GDP . . . D 4 10.522 23.043 7.389 1 53.17 ? C6 GDP 402 A 1 HETATM 23 O O6 GDP . . . D 4 11.447 22.303 7.009 1 54.24 ? O6 GDP 402 A 1 HETATM 24 N N1 GDP . . . D 4 9.579 22.59 8.218 1 54.16 ? N1 GDP 402 A 1 HETATM 25 C C2 GDP . . . D 4 8.57 23.367 8.637 1 52.57 ? C2 GDP 402 A 1 HETATM 26 N N2 GDP . . . D 4 7.655 22.834 9.474 1 50.22 ? N2 GDP 402 A 1 HETATM 27 N N3 GDP . . . D 4 8.43 24.657 8.262 1 51.93 ? N3 GDP 402 A 1 HETATM 28 C C4 GDP . . . D 4 9.318 25.236 7.429 1 52.63 ? C4 GDP 402 A 1 HETATM 29 H H4' GDP . . . D 4 9.08 30.544 7.347 1 85.61 ? H4' GDP 402 A 1 HETATM 30 H H3' GDP . . . D 4 10.761 28.402 8.603 1 82.12 ? H3' GDP 402 A 1 HETATM 31 H HO3' GDP . . . D 4 9.727 29.365 10.495 1 80.02 ? HO3' GDP 402 A 1 HETATM 32 H H2' GDP . . . D 4 8.94 27.075 9.179 1 81.15 ? H2' GDP 402 A 1 HETATM 33 H HO2' GDP . . . D 4 7.641 28.961 9.934 1 77.09 ? HO2' GDP 402 A 1 HETATM 34 H H1' GDP . . . D 4 7.498 27.31 6.892 1 78.28 ? H1' GDP 402 A 1 HETATM 35 H H8 GDP . . . D 4 10.899 27.312 5.558 1 63.34 ? H8 GDP 402 A 1 HETATM 36 H HN1 GDP . . . D 4 9.624 21.604 8.545 1 64.99 ? HN1 GDP 402 A 1 HETATM 37 H HN21 GDP . . . D 4 6.887 23.398 9.807 1 60.26 ? HN21 GDP 402 A 1 HETATM 38 H HN22 GDP . . . D 4 7.74 21.872 9.768 1 60.26 ? HN22 GDP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 38 #