data_6YPK # _model_server_result.job_id HBBVuX0mKhQiS07cGhSPmg _model_server_result.datetime_utc '2024-11-26 12:56:00' _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 6ypk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6YPK # _exptl.entry_id 6YPK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 110.98 _cell.angle_gamma 90 _cell.entry_id 6YPK _cell.length_a 57.7 _cell.length_b 45.37 _cell.length_c 63.49 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YPK _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 PISA _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 6YPK _atom_sites.fract_transf_matrix[1][1] 0.017331 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006646 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022041 _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] 0.016869 _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 GDP A 1 401 401 GDP GDP . C 3 HOH A 1 501 151 HOH HOH . C 3 HOH A 2 502 73 HOH HOH . C 3 HOH A 3 503 42 HOH HOH . C 3 HOH A 4 504 110 HOH HOH . C 3 HOH A 5 505 161 HOH HOH . C 3 HOH A 6 506 11 HOH HOH . C 3 HOH A 7 507 159 HOH HOH . C 3 HOH A 8 508 12 HOH HOH . C 3 HOH A 9 509 64 HOH HOH . C 3 HOH A 10 510 4 HOH HOH . C 3 HOH A 11 511 43 HOH HOH . C 3 HOH A 12 512 48 HOH HOH . C 3 HOH A 13 513 22 HOH HOH . C 3 HOH A 14 514 85 HOH HOH . C 3 HOH A 15 515 91 HOH HOH . C 3 HOH A 16 516 39 HOH HOH . C 3 HOH A 17 517 46 HOH HOH . C 3 HOH A 18 518 78 HOH HOH . C 3 HOH A 19 519 34 HOH HOH . C 3 HOH A 20 520 26 HOH HOH . C 3 HOH A 21 521 41 HOH HOH . C 3 HOH A 22 522 74 HOH HOH . C 3 HOH A 23 523 50 HOH HOH . C 3 HOH A 24 524 94 HOH HOH . C 3 HOH A 25 525 19 HOH HOH . C 3 HOH A 26 526 109 HOH HOH . C 3 HOH A 27 527 23 HOH HOH . C 3 HOH A 28 528 9 HOH HOH . C 3 HOH A 29 529 155 HOH HOH . C 3 HOH A 30 530 21 HOH HOH . C 3 HOH A 31 531 45 HOH HOH . C 3 HOH A 32 532 127 HOH HOH . C 3 HOH A 33 533 152 HOH HOH . C 3 HOH A 34 534 68 HOH HOH . C 3 HOH A 35 535 86 HOH HOH . C 3 HOH A 36 536 76 HOH HOH . C 3 HOH A 37 537 72 HOH HOH . C 3 HOH A 38 538 25 HOH HOH . C 3 HOH A 39 539 15 HOH HOH . C 3 HOH A 40 540 32 HOH HOH . C 3 HOH A 41 541 96 HOH HOH . C 3 HOH A 42 542 92 HOH HOH . C 3 HOH A 43 543 84 HOH HOH . C 3 HOH A 44 544 120 HOH HOH . C 3 HOH A 45 545 107 HOH HOH . C 3 HOH A 46 546 49 HOH HOH . C 3 HOH A 47 547 122 HOH HOH . C 3 HOH A 48 548 124 HOH HOH . C 3 HOH A 49 549 106 HOH HOH . C 3 HOH A 50 550 14 HOH HOH . C 3 HOH A 51 551 156 HOH HOH . C 3 HOH A 52 552 37 HOH HOH . C 3 HOH A 53 553 142 HOH HOH . C 3 HOH A 54 554 82 HOH HOH . C 3 HOH A 55 555 115 HOH HOH . C 3 HOH A 56 556 140 HOH HOH . C 3 HOH A 57 557 65 HOH HOH . C 3 HOH A 58 558 148 HOH HOH . C 3 HOH A 59 559 6 HOH HOH . C 3 HOH A 60 560 2 HOH HOH . C 3 HOH A 61 561 1 HOH HOH . C 3 HOH A 62 562 56 HOH HOH . C 3 HOH A 63 563 135 HOH HOH . C 3 HOH A 64 564 102 HOH HOH . C 3 HOH A 65 565 13 HOH HOH . C 3 HOH A 66 566 62 HOH HOH . C 3 HOH A 67 567 8 HOH HOH . C 3 HOH A 68 568 153 HOH HOH . C 3 HOH A 69 569 18 HOH HOH . C 3 HOH A 70 570 128 HOH HOH . C 3 HOH A 71 571 137 HOH HOH . C 3 HOH A 72 572 51 HOH HOH . C 3 HOH A 73 573 3 HOH HOH . C 3 HOH A 74 574 10 HOH HOH . C 3 HOH A 75 575 130 HOH HOH . C 3 HOH A 76 576 67 HOH HOH . C 3 HOH A 77 577 97 HOH HOH . C 3 HOH A 78 578 132 HOH HOH . C 3 HOH A 79 579 75 HOH HOH . C 3 HOH A 80 580 17 HOH HOH . C 3 HOH A 81 581 117 HOH HOH . C 3 HOH A 82 582 47 HOH HOH . C 3 HOH A 83 583 89 HOH HOH . C 3 HOH A 84 584 58 HOH HOH . C 3 HOH A 85 585 16 HOH HOH . C 3 HOH A 86 586 69 HOH HOH . C 3 HOH A 87 587 5 HOH HOH . C 3 HOH A 88 588 88 HOH HOH . C 3 HOH A 89 589 116 HOH HOH . C 3 HOH A 90 590 112 HOH HOH . C 3 HOH A 91 591 103 HOH HOH . C 3 HOH A 92 592 114 HOH HOH . C 3 HOH A 93 593 71 HOH HOH . C 3 HOH A 94 594 113 HOH HOH . C 3 HOH A 95 595 98 HOH HOH . C 3 HOH A 96 596 129 HOH HOH . C 3 HOH A 97 597 145 HOH HOH . C 3 HOH A 98 598 158 HOH HOH . C 3 HOH A 99 599 31 HOH HOH . C 3 HOH A 100 600 131 HOH HOH . C 3 HOH A 101 601 79 HOH HOH . C 3 HOH A 102 602 157 HOH HOH . C 3 HOH A 103 603 104 HOH HOH . C 3 HOH A 104 604 29 HOH HOH . C 3 HOH A 105 605 60 HOH HOH . C 3 HOH A 106 606 40 HOH HOH . C 3 HOH A 107 607 33 HOH HOH . C 3 HOH A 108 608 36 HOH HOH . C 3 HOH A 109 609 70 HOH HOH . C 3 HOH A 110 610 53 HOH HOH . C 3 HOH A 111 611 55 HOH HOH . C 3 HOH A 112 612 81 HOH HOH . C 3 HOH A 113 613 136 HOH HOH . C 3 HOH A 114 614 66 HOH HOH . C 3 HOH A 115 615 44 HOH HOH . C 3 HOH A 116 616 80 HOH HOH . C 3 HOH A 117 617 119 HOH HOH . C 3 HOH A 118 618 146 HOH HOH . C 3 HOH A 119 619 57 HOH HOH . C 3 HOH A 120 620 147 HOH HOH . C 3 HOH A 121 621 149 HOH HOH . C 3 HOH A 122 622 77 HOH HOH . C 3 HOH A 123 623 141 HOH HOH . C 3 HOH A 124 624 118 HOH HOH . C 3 HOH A 125 625 111 HOH HOH . C 3 HOH A 126 626 90 HOH HOH . C 3 HOH A 127 627 150 HOH HOH . C 3 HOH A 128 628 105 HOH HOH . C 3 HOH A 129 629 101 HOH HOH . C 3 HOH A 130 630 99 HOH HOH . C 3 HOH A 131 631 93 HOH HOH . C 3 HOH A 132 632 123 HOH HOH . C 3 HOH A 133 633 138 HOH HOH . C 3 HOH A 134 634 87 HOH HOH . C 3 HOH A 135 635 133 HOH HOH . C 3 HOH A 136 636 139 HOH HOH . C 3 HOH A 137 637 154 HOH HOH . C 3 HOH A 138 638 38 HOH HOH . C 3 HOH A 139 639 61 HOH HOH . C 3 HOH A 140 640 134 HOH HOH . C 3 HOH A 141 641 160 HOH HOH . C 3 HOH A 142 642 108 HOH HOH . C 3 HOH A 143 643 63 HOH HOH . C 3 HOH A 144 644 125 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 . . . B 2 -114.853 -198.693 300.979 1 57.32 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 -115.171 -197.832 299.725 1 59.39 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 -113.516 -199.342 300.919 1 56.08 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 -116.019 -199.661 301.212 1 60.31 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 -114.927 -197.708 302.227 1 52.29 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 -113.886 -196.651 302.805 1 43.85 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 -112.877 -196.326 301.715 1 43.76 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 -113.288 -197.217 304.032 1 40.24 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 -114.658 -195.294 303.108 1 42.78 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 -115.181 -194.498 302.028 1 42.79 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 -116.673 -194.416 302.218 1 43.85 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 -116.943 -193.737 303.456 1 41.17 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 -117.409 -193.6 301.164 1 45.36 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 -117.71 -194.411 300.032 1 45.35 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 -118.663 -193.128 301.91 1 46.71 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 -119.777 -193.992 301.699 1 51.38 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 -118.228 -193.158 303.388 1 42.08 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 -118.185 -191.849 304.057 1 37.51 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 -117.459 -190.735 303.714 1 35.17 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 -117.683 -189.701 304.494 1 32.91 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 -118.617 -190.162 305.406 1 33.67 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 -119.248 -189.519 306.511 1 36.4 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 -119.119 -188.349 306.858 1 39.88 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 -120.054 -190.38 307.233 1 35.2 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 -120.237 -191.712 306.952 1 34.46 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 -120.934 -192.429 307.84 1 32.53 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 -119.696 -192.319 305.897 1 33.31 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 -118.915 -191.494 305.165 1 34.97 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #