data_8RSQ # _model_server_result.job_id O46T9nR9kogSXE76zMgJrw _model_server_result.datetime_utc '2025-06-20 01:06:17' _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 8rsq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8RSQ # _exptl.entry_id 8RSQ _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 124.63 _cell.angle_gamma 90 _cell.entry_id 8RSQ _cell.length_a 132.856 _cell.length_b 39.718 _cell.length_c 94.984 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RSQ _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,G,H,I,J,K,L _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 K _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 510 _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 1.451 _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 8RSQ _atom_sites.fract_transf_matrix[1][1] 0.007527 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005198 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025178 _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] 0.012795 _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 1 502 601 LFA LFA . D 3 LFA A 1 503 602 LFA LFA . E 3 LFA A 1 504 603 LFA LFA . F 3 LFA A 1 505 604 LFA LFA . G 3 LFA A 1 506 605 LFA LFA . H 3 LFA A 1 507 606 LFA LFA . I 3 LFA A 1 508 607 LFA LFA . J 3 LFA A 1 509 608 LFA LFA . K 4 RET A 1 510 200 RET LYR . L 5 HOH A 1 601 502 HOH HOH . L 5 HOH A 2 602 756 HOH HOH . L 5 HOH A 3 603 752 HOH HOH . L 5 HOH A 4 604 765 HOH HOH . L 5 HOH A 5 605 775 HOH HOH . L 5 HOH A 6 606 782 HOH HOH . L 5 HOH A 7 607 746 HOH HOH . L 5 HOH A 8 608 797 HOH HOH . L 5 HOH A 9 609 760 HOH HOH . L 5 HOH A 10 610 755 HOH HOH . L 5 HOH A 11 611 750 HOH HOH . L 5 HOH A 12 612 734 HOH HOH . L 5 HOH A 13 613 798 HOH HOH . L 5 HOH A 14 614 757 HOH HOH . L 5 HOH A 15 615 738 HOH HOH . L 5 HOH A 16 616 701 HOH HOH . L 5 HOH A 17 617 754 HOH HOH . L 5 HOH A 18 618 796 HOH HOH . L 5 HOH A 19 619 728 HOH HOH . L 5 HOH A 20 620 706 HOH HOH . L 5 HOH A 21 621 791 HOH HOH . L 5 HOH A 22 622 717 HOH HOH . L 5 HOH A 23 623 712 HOH HOH . L 5 HOH A 24 624 769 HOH HOH . L 5 HOH A 25 625 719 HOH HOH . L 5 HOH A 26 626 747 HOH HOH . L 5 HOH A 27 627 786 HOH HOH . L 5 HOH A 28 628 743 HOH HOH . L 5 HOH A 29 629 735 HOH HOH . L 5 HOH A 30 630 742 HOH HOH . L 5 HOH A 31 631 748 HOH HOH . L 5 HOH A 32 632 730 HOH HOH . L 5 HOH A 33 633 794 HOH HOH . L 5 HOH A 34 634 784 HOH HOH . L 5 HOH A 35 635 762 HOH HOH . L 5 HOH A 36 636 758 HOH HOH . L 5 HOH A 37 637 761 HOH HOH . L 5 HOH A 38 638 709 HOH HOH . L 5 HOH A 39 639 795 HOH HOH . L 5 HOH A 40 640 715 HOH HOH . L 5 HOH A 41 641 764 HOH HOH . L 5 HOH A 42 642 506 HOH HOH . L 5 HOH A 43 643 763 HOH HOH . L 5 HOH A 44 644 708 HOH HOH . L 5 HOH A 45 645 770 HOH HOH . L 5 HOH A 46 646 507 HOH HOH . L 5 HOH A 47 647 703 HOH HOH . L 5 HOH A 48 648 789 HOH HOH . L 5 HOH A 49 649 724 HOH HOH . L 5 HOH A 50 650 733 HOH HOH . L 5 HOH A 51 651 729 HOH HOH . L 5 HOH A 52 652 704 HOH HOH . L 5 HOH A 53 653 705 HOH HOH . L 5 HOH A 54 654 713 HOH HOH . L 5 HOH A 55 655 790 HOH HOH . L 5 HOH A 56 656 726 HOH HOH . L 5 HOH A 57 657 727 HOH HOH . L 5 HOH A 58 658 505 HOH HOH . L 5 HOH A 59 659 740 HOH HOH . L 5 HOH A 60 660 737 HOH HOH . L 5 HOH A 61 661 744 HOH HOH . L 5 HOH A 62 662 751 HOH HOH . L 5 HOH A 63 663 792 HOH HOH . L 5 HOH A 64 664 783 HOH HOH . L 5 HOH A 65 665 718 HOH HOH . L 5 HOH A 66 666 732 HOH HOH . L 5 HOH A 67 667 723 HOH HOH . L 5 HOH A 68 668 771 HOH HOH . L 5 HOH A 69 669 721 HOH HOH . L 5 HOH A 70 670 776 HOH HOH . L 5 HOH A 71 671 793 HOH HOH . L 5 HOH A 72 672 2 HOH HOH . L 5 HOH A 73 673 722 HOH HOH . L 5 HOH A 74 674 711 HOH HOH . L 5 HOH A 75 675 736 HOH HOH . L 5 HOH A 76 676 710 HOH HOH . L 5 HOH A 77 677 1 HOH HOH . L 5 HOH A 78 678 707 HOH HOH . L 5 HOH A 79 679 777 HOH HOH . L 5 HOH A 80 680 779 HOH HOH . L 5 HOH A 81 681 753 HOH HOH . L 5 HOH A 82 682 749 HOH HOH . L 5 HOH A 83 683 787 HOH HOH . L 5 HOH A 84 684 720 HOH HOH . L 5 HOH A 85 685 509 HOH HOH . L 5 HOH A 86 686 731 HOH HOH . L 5 HOH A 87 687 714 HOH HOH . L 5 HOH A 88 688 778 HOH HOH . L 5 HOH A 89 689 508 HOH HOH . L 5 HOH A 90 690 785 HOH HOH . L 5 HOH A 91 691 503 HOH HOH . L 5 HOH A 92 692 774 HOH HOH . L 5 HOH A 93 693 739 HOH HOH . L 5 HOH A 94 694 766 HOH HOH . L 5 HOH A 95 695 773 HOH HOH . L 5 HOH A 96 696 716 HOH HOH . L 5 HOH A 97 697 767 HOH HOH . L 5 HOH A 98 698 725 HOH HOH . L 5 HOH A 99 699 759 HOH HOH . L 5 HOH A 100 700 781 HOH HOH . L 5 HOH A 101 701 780 HOH HOH . L 5 HOH A 102 702 741 HOH HOH . L 5 HOH A 103 703 768 HOH HOH . L 5 HOH A 104 704 504 HOH HOH . L 5 HOH A 105 705 788 HOH HOH . L 5 HOH A 106 706 745 HOH HOH . L 5 HOH A 107 707 772 HOH HOH . L 5 HOH A 108 708 702 HOH HOH . L 5 HOH A 109 709 510 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 45.224 -17.165 -6.782 1 28.71 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 45.601 -17.454 -8.214 1 28.31 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 46.366 -16.443 -6.106 1 33.28 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 43.983 -16.308 -6.757 1 21.66 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 44.951 -18.544 -6.001 1 30.04 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 43.493 -19.224 -5.961 1 32.27 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 42.816 -19.195 -7.31 1 20.63 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 42.636 -18.554 -4.913 1 26.56 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 43.836 -20.731 -5.516 1 38.73 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 43.936 -21.766 -6.49 1 39.38 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 43.633 -23.097 -5.822 1 41.29 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 44.289 -23.163 -4.553 1 34.77 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 42.141 -23.235 -5.571 1 38.92 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 41.659 -24.425 -6.201 1 43.7 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 41.993 -23.354 -4.069 1 33.44 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 41.058 -24.383 -3.739 1 51.71 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 43.39 -23.701 -3.58 1 37.46 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 43.637 -23.119 -2.237 1 38.96 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 43.7 -21.81 -1.928 1 37.78 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 43.944 -21.634 -0.603 1 36.23 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 44.048 -22.855 -0.045 1 31.88 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 44.301 -23.397 1.311 1 37 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 44.482 -22.635 2.285 1 34.76 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 44.329 -24.728 1.461 1 37.01 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 44.136 -25.574 0.431 1 47.61 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 44.18 -26.908 0.666 1 48.3 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 43.9 -25.148 -0.836 1 45.71 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 43.846 -23.827 -1.128 1 40.03 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #