data_8RSR # _model_server_result.job_id 0rTnTjftPNffKfvRhKmDGQ _model_server_result.datetime_utc '2025-08-03 04:28:38' _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 8rsr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8RSR # _exptl.entry_id 8RSR _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 124.54 _cell.angle_gamma 90 _cell.entry_id 8RSR _cell.length_a 133.186 _cell.length_b 39.787 _cell.length_c 95.756 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RSR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 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,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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 200 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 200 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 504 _struct_conn.ptnr2_symmetry 1_555 _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 1.449 _struct_conn.pdbx_value_order sing # _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 8RSR _atom_sites.fract_transf_matrix[1][1] 0.007508 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005168 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025134 _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] 0.012678 _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 1 501 501 GDP GDP . C 3 LFA A 1 502 502 LFA LFA . D 4 OLA A 1 503 1 OLA OLA . E 5 RET A 1 504 200 RET LYR . F 6 HOH A 1 601 553 HOH HOH . F 6 HOH A 2 602 540 HOH HOH . F 6 HOH A 3 603 544 HOH HOH . F 6 HOH A 4 604 4 HOH HOH . F 6 HOH A 5 605 50 HOH HOH . F 6 HOH A 6 606 503 HOH HOH . F 6 HOH A 7 607 523 HOH HOH . F 6 HOH A 8 608 532 HOH HOH . F 6 HOH A 9 609 47 HOH HOH . F 6 HOH A 10 610 13 HOH HOH . F 6 HOH A 11 611 7 HOH HOH . F 6 HOH A 12 612 23 HOH HOH . F 6 HOH A 13 613 43 HOH HOH . F 6 HOH A 14 614 543 HOH HOH . F 6 HOH A 15 615 9 HOH HOH . F 6 HOH A 16 616 539 HOH HOH . F 6 HOH A 17 617 517 HOH HOH . F 6 HOH A 18 618 518 HOH HOH . F 6 HOH A 19 619 3 HOH HOH . F 6 HOH A 20 620 16 HOH HOH . F 6 HOH A 21 621 521 HOH HOH . F 6 HOH A 22 622 59 HOH HOH . F 6 HOH A 23 623 547 HOH HOH . F 6 HOH A 24 624 538 HOH HOH . F 6 HOH A 25 625 64 HOH HOH . F 6 HOH A 26 626 33 HOH HOH . F 6 HOH A 27 627 526 HOH HOH . F 6 HOH A 28 628 546 HOH HOH . F 6 HOH A 29 629 57 HOH HOH . F 6 HOH A 30 630 536 HOH HOH . F 6 HOH A 31 631 527 HOH HOH . F 6 HOH A 32 632 524 HOH HOH . F 6 HOH A 33 633 529 HOH HOH . F 6 HOH A 34 634 512 HOH HOH . F 6 HOH A 35 635 525 HOH HOH . F 6 HOH A 36 636 530 HOH HOH . F 6 HOH A 37 637 508 HOH HOH . F 6 HOH A 38 638 511 HOH HOH . F 6 HOH A 39 639 24 HOH HOH . F 6 HOH A 40 640 506 HOH HOH . F 6 HOH A 41 641 558 HOH HOH . F 6 HOH A 42 642 528 HOH HOH . F 6 HOH A 43 643 2 HOH HOH . F 6 HOH A 44 644 49 HOH HOH . F 6 HOH A 45 645 531 HOH HOH . F 6 HOH A 46 646 60 HOH HOH . F 6 HOH A 47 647 22 HOH HOH . F 6 HOH A 48 648 505 HOH HOH . F 6 HOH A 49 649 44 HOH HOH . F 6 HOH A 50 650 545 HOH HOH . F 6 HOH A 51 651 63 HOH HOH . F 6 HOH A 52 652 537 HOH HOH . F 6 HOH A 53 653 555 HOH HOH . F 6 HOH A 54 654 30 HOH HOH . F 6 HOH A 55 655 520 HOH HOH . F 6 HOH A 56 656 509 HOH HOH . F 6 HOH A 57 657 28 HOH HOH . F 6 HOH A 58 658 35 HOH HOH . F 6 HOH A 59 659 51 HOH HOH . F 6 HOH A 60 660 510 HOH HOH . F 6 HOH A 61 661 40 HOH HOH . F 6 HOH A 62 662 557 HOH HOH . F 6 HOH A 63 663 36 HOH HOH . F 6 HOH A 64 664 41 HOH HOH . F 6 HOH A 65 665 548 HOH HOH . F 6 HOH A 66 666 515 HOH HOH . F 6 HOH A 67 667 56 HOH HOH . F 6 HOH A 68 668 8 HOH HOH . F 6 HOH A 69 669 5 HOH HOH . F 6 HOH A 70 670 522 HOH HOH . F 6 HOH A 71 671 549 HOH HOH . F 6 HOH A 72 672 551 HOH HOH . F 6 HOH A 73 673 27 HOH HOH . F 6 HOH A 74 674 542 HOH HOH . F 6 HOH A 75 675 535 HOH HOH . F 6 HOH A 76 676 62 HOH HOH . F 6 HOH A 77 677 507 HOH HOH . F 6 HOH A 78 678 541 HOH HOH . F 6 HOH A 79 679 55 HOH HOH . F 6 HOH A 80 680 513 HOH HOH . F 6 HOH A 81 681 58 HOH HOH . F 6 HOH A 82 682 17 HOH HOH . F 6 HOH A 83 683 18 HOH HOH . F 6 HOH A 84 684 10 HOH HOH . F 6 HOH A 85 685 42 HOH HOH . F 6 HOH A 86 686 61 HOH HOH . F 6 HOH A 87 687 26 HOH HOH . F 6 HOH A 88 688 45 HOH HOH . F 6 HOH A 89 689 54 HOH HOH . F 6 HOH A 90 690 39 HOH HOH . F 6 HOH A 91 691 52 HOH HOH . F 6 HOH A 92 692 32 HOH HOH . F 6 HOH A 93 693 1 HOH HOH . F 6 HOH A 94 694 25 HOH HOH . F 6 HOH A 95 695 38 HOH HOH . F 6 HOH A 96 696 37 HOH HOH . F 6 HOH A 97 697 31 HOH HOH . F 6 HOH A 98 698 519 HOH HOH . F 6 HOH A 99 699 29 HOH HOH . F 6 HOH A 100 700 53 HOH HOH . F 6 HOH A 101 701 46 HOH HOH . F 6 HOH A 102 702 15 HOH HOH . F 6 HOH A 103 703 552 HOH HOH . F 6 HOH A 104 704 554 HOH HOH . F 6 HOH A 105 705 48 HOH HOH . F 6 HOH A 106 706 550 HOH HOH . F 6 HOH A 107 707 34 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 -21.3 2.716 -6.886 1 38.27 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 -20.997 2.324 -8.313 1 39.81 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 -20.105 3.419 -6.289 1 39.72 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 -22.497 3.635 -6.881 1 38.7 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 -21.608 1.406 -6.006 1 39.34 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 -23.055 0.697 -6.017 1 39.65 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 -23.683 0.748 -7.389 1 41.8 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 -23.96 1.325 -4.984 1 40.72 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 -22.686 -0.808 -5.585 1 42.54 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 -22.746 -1.873 -6.531 1 43.92 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 -22.9 -3.185 -5.781 1 47.2 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 -22.18 -3.139 -4.544 1 46.96 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 -24.361 -3.427 -5.44 1 48.51 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 -24.849 -4.565 -6.156 1 50.83 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 -24.394 -3.705 -3.953 1 49.11 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 -25.098 -4.923 -3.695 1 56.44 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 -22.934 -3.815 -3.536 1 47.54 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 -22.759 -3.207 -2.195 1 46.27 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 -22.779 -1.894 -1.895 1 44.44 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 -22.592 -1.695 -0.563 1 44.56 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 -22.446 -2.905 0.009 1 46.96 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 -22.216 -3.423 1.378 1 48.73 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 -22.11 -2.642 2.348 1 49.14 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 -22.125 -4.749 1.542 1 49.52 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 -22.237 -5.612 0.512 1 50.44 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 -22.133 -6.941 0.759 1 53.32 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 -22.449 -5.208 -0.767 1 49.26 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 -22.558 -3.894 -1.071 1 46.68 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #