data_4DCS # _model_server_result.job_id 2qB74NAW2woiBy-BFsqdwA _model_server_result.datetime_utc '2025-01-03 03:27:00' _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 4dcs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4DCS # _exptl.entry_id 4DCS _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 90 _cell.angle_gamma 90 _cell.entry_id 4DCS _cell.length_a 63.3 _cell.length_b 65.79 _cell.length_c 111.43 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DCS _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 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 _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 4DCS _atom_sites.fract_transf_matrix[1][1] 0.015798 _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] 0.0152 _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] 0.008974 _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 1 501 500 GDP GDP . C 3 SO4 A 1 502 1 SO4 SO4 . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 11 HOH HOH . D 4 HOH A 12 612 12 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 14 HOH HOH . D 4 HOH A 15 615 15 HOH HOH . D 4 HOH A 16 616 16 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 18 HOH HOH . D 4 HOH A 19 619 19 HOH HOH . D 4 HOH A 20 620 20 HOH HOH . D 4 HOH A 21 621 21 HOH HOH . D 4 HOH A 22 622 23 HOH HOH . D 4 HOH A 23 623 24 HOH HOH . D 4 HOH A 24 624 25 HOH HOH . D 4 HOH A 25 625 26 HOH HOH . D 4 HOH A 26 626 27 HOH HOH . D 4 HOH A 27 627 28 HOH HOH . D 4 HOH A 28 628 29 HOH HOH . D 4 HOH A 29 629 30 HOH HOH . D 4 HOH A 30 630 31 HOH HOH . D 4 HOH A 31 631 32 HOH HOH . D 4 HOH A 32 632 33 HOH HOH . D 4 HOH A 33 633 34 HOH HOH . D 4 HOH A 34 634 35 HOH HOH . D 4 HOH A 35 635 36 HOH HOH . D 4 HOH A 36 636 37 HOH HOH . D 4 HOH A 37 637 39 HOH HOH . D 4 HOH A 38 638 40 HOH HOH . D 4 HOH A 39 639 41 HOH HOH . D 4 HOH A 40 640 43 HOH HOH . D 4 HOH A 41 641 44 HOH HOH . D 4 HOH A 42 642 45 HOH HOH . D 4 HOH A 43 643 46 HOH HOH . D 4 HOH A 44 644 47 HOH HOH . D 4 HOH A 45 645 48 HOH HOH . D 4 HOH A 46 646 50 HOH HOH . D 4 HOH A 47 647 51 HOH HOH . D 4 HOH A 48 648 52 HOH HOH . D 4 HOH A 49 649 53 HOH HOH . D 4 HOH A 50 650 54 HOH HOH . D 4 HOH A 51 651 55 HOH HOH . D 4 HOH A 52 652 56 HOH HOH . D 4 HOH A 53 653 57 HOH HOH . D 4 HOH A 54 654 58 HOH HOH . D 4 HOH A 55 655 59 HOH HOH . D 4 HOH A 56 656 60 HOH HOH . D 4 HOH A 57 657 61 HOH HOH . D 4 HOH A 58 658 62 HOH HOH . D 4 HOH A 59 659 63 HOH HOH . D 4 HOH A 60 660 64 HOH HOH . D 4 HOH A 61 661 65 HOH HOH . D 4 HOH A 62 662 66 HOH HOH . D 4 HOH A 63 663 67 HOH HOH . D 4 HOH A 64 664 68 HOH HOH . D 4 HOH A 65 665 69 HOH HOH . D 4 HOH A 66 666 70 HOH HOH . D 4 HOH A 67 667 72 HOH HOH . D 4 HOH A 68 668 73 HOH HOH . D 4 HOH A 69 669 74 HOH HOH . D 4 HOH A 70 670 75 HOH HOH . D 4 HOH A 71 671 76 HOH HOH . D 4 HOH A 72 672 77 HOH HOH . D 4 HOH A 73 673 78 HOH HOH . D 4 HOH A 74 674 79 HOH HOH . D 4 HOH A 75 675 80 HOH HOH . D 4 HOH A 76 676 81 HOH HOH . D 4 HOH A 77 677 82 HOH HOH . D 4 HOH A 78 678 83 HOH HOH . D 4 HOH A 79 679 84 HOH HOH . D 4 HOH A 80 680 85 HOH HOH . D 4 HOH A 81 681 86 HOH HOH . D 4 HOH A 82 682 87 HOH HOH . D 4 HOH A 83 683 88 HOH HOH . D 4 HOH A 84 684 89 HOH HOH . D 4 HOH A 85 685 90 HOH HOH . D 4 HOH A 86 686 91 HOH HOH . D 4 HOH A 87 687 92 HOH HOH . D 4 HOH A 88 688 93 HOH HOH . D 4 HOH A 89 689 94 HOH HOH . D 4 HOH A 90 690 95 HOH HOH . D 4 HOH A 91 691 96 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 -14.127 -8.568 -33.783 1 37.65 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 -14.387 -7.105 -34.025 1 38.26 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 -12.886 -9.049 -34.498 1 37.64 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 -14.22 -8.998 -32.342 1 37.5 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 -15.316 -9.342 -34.54 1 35.62 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 -16.606 -9.989 -33.831 1 37.04 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 -16.296 -11.295 -33.139 1 36.43 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 -17.348 -8.917 -33.059 1 39 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 -17.469 -10.39 -35.132 1 37.51 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 -17.85 -9.452 -36.142 1 36.99 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 -18.982 -10.046 -36.974 1 36.23 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 -18.497 -11.136 -37.771 1 36.41 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 -20.091 -10.606 -36.091 1 37.11 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 -21.35 -10.314 -36.69 1 38.08 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 -19.901 -12.108 -36.149 1 38.09 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 -21.136 -12.81 -35.996 1 39.96 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 -19.292 -12.311 -37.53 1 36.5 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 -18.495 -13.558 -37.536 1 36.2 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 -17.52 -13.877 -36.661 1 34.42 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 -17 -15.098 -36.944 1 34.8 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 -17.64 -15.58 -38.024 1 33.91 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 -17.572 -16.809 -38.848 1 33.27 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 -16.765 -17.725 -38.594 1 31.04 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 -18.423 -16.918 -39.878 1 34.47 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 -19.314 -15.957 -40.201 1 35.1 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 -20.121 -16.157 -41.278 1 34.17 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 -19.413 -14.797 -39.492 1 34.3 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 -18.629 -14.563 -38.411 1 34.96 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #