data_2GEK # _model_server_result.job_id HbwEwPuo8srJU5QZGXIN7A _model_server_result.datetime_utc '2024-12-21 12:11:31' _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 2gek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2567}' # _entry.id 2GEK # _exptl.entry_id 2GEK _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 2GEK _cell.length_a 37.176 _cell.length_b 72.425 _cell.length_c 138.23 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GEK _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 2GEK _atom_sites.fract_transf_matrix[1][1] 0.0269 _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] 0.01381 _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] 0.00723 _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 2567 2567 GDP GDP . C 3 HOH A 1 2568 1 HOH HOH . C 3 HOH A 2 2569 2 HOH HOH . C 3 HOH A 3 2570 3 HOH HOH . C 3 HOH A 4 2571 4 HOH HOH . C 3 HOH A 5 2572 5 HOH HOH . C 3 HOH A 6 2573 6 HOH HOH . C 3 HOH A 7 2574 7 HOH HOH . C 3 HOH A 8 2575 8 HOH HOH . C 3 HOH A 9 2576 9 HOH HOH . C 3 HOH A 10 2577 10 HOH HOH . C 3 HOH A 11 2578 11 HOH HOH . C 3 HOH A 12 2579 12 HOH HOH . C 3 HOH A 13 2580 13 HOH HOH . C 3 HOH A 14 2581 14 HOH HOH . C 3 HOH A 15 2582 15 HOH HOH . C 3 HOH A 16 2583 16 HOH HOH . C 3 HOH A 17 2584 17 HOH HOH . C 3 HOH A 18 2585 18 HOH HOH . C 3 HOH A 19 2586 19 HOH HOH . C 3 HOH A 20 2587 20 HOH HOH . C 3 HOH A 21 2588 21 HOH HOH . C 3 HOH A 22 2589 22 HOH HOH . C 3 HOH A 23 2590 23 HOH HOH . C 3 HOH A 24 2591 24 HOH HOH . C 3 HOH A 25 2592 25 HOH HOH . C 3 HOH A 26 2593 26 HOH HOH . C 3 HOH A 27 2594 27 HOH HOH . C 3 HOH A 28 2595 28 HOH HOH . C 3 HOH A 29 2596 29 HOH HOH . C 3 HOH A 30 2597 30 HOH HOH . C 3 HOH A 31 2598 31 HOH HOH . C 3 HOH A 32 2599 32 HOH HOH . C 3 HOH A 33 2600 33 HOH HOH . C 3 HOH A 34 2601 34 HOH HOH . C 3 HOH A 35 2602 35 HOH HOH . C 3 HOH A 36 2603 36 HOH HOH . C 3 HOH A 37 2604 37 HOH HOH . C 3 HOH A 38 2605 38 HOH HOH . C 3 HOH A 39 2606 39 HOH HOH . C 3 HOH A 40 2607 40 HOH HOH . C 3 HOH A 41 2608 41 HOH HOH . C 3 HOH A 42 2609 42 HOH HOH . C 3 HOH A 43 2610 43 HOH HOH . C 3 HOH A 44 2611 44 HOH HOH . C 3 HOH A 45 2612 45 HOH HOH . C 3 HOH A 46 2613 46 HOH HOH . C 3 HOH A 47 2614 47 HOH HOH . C 3 HOH A 48 2615 48 HOH HOH . C 3 HOH A 49 2616 49 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 -5.164 43.972 28.804 1 45.7 ? PB GDP 2567 A 1 HETATM 2 O O1B GDP . . . B 2 -5.178 45.416 29.262 1 42.46 ? O1B GDP 2567 A 1 HETATM 3 O O2B GDP . . . B 2 -6.398 43.509 29.576 1 43.87 ? O2B GDP 2567 A 1 HETATM 4 O O3B GDP . . . B 2 -5.152 43.849 27.273 1 42.75 ? O3B GDP 2567 A 1 HETATM 5 O O3A GDP . . . B 2 -3.955 42.937 29.27 1 43.35 ? O3A GDP 2567 A 1 HETATM 6 P PA GDP . . . B 2 -2.691 43.572 30.008 1 39.21 ? PA GDP 2567 A 1 HETATM 7 O O1A GDP . . . B 2 -2.889 45.029 29.716 1 46.65 ? O1A GDP 2567 A 1 HETATM 8 O O2A GDP . . . B 2 -2.649 43.56 31.533 1 37.91 ? O2A GDP 2567 A 1 HETATM 9 O O5' GDP . . . B 2 -1.368 43.196 29.171 1 35.63 ? O5' GDP 2567 A 1 HETATM 10 C C5' GDP . . . B 2 -1.193 43.914 27.968 1 31.49 ? C5' GDP 2567 A 1 HETATM 11 C C4' GDP . . . B 2 0.211 44.366 27.574 1 31.42 ? C4' GDP 2567 A 1 HETATM 12 O O4' GDP . . . B 2 0.32 45.77 27.763 1 33.27 ? O4' GDP 2567 A 1 HETATM 13 C C3' GDP . . . B 2 1.385 43.768 28.291 1 29.79 ? C3' GDP 2567 A 1 HETATM 14 O O3' GDP . . . B 2 2.359 43.77 27.268 1 26.11 ? O3' GDP 2567 A 1 HETATM 15 C C2' GDP . . . B 2 1.697 44.799 29.348 1 31.64 ? C2' GDP 2567 A 1 HETATM 16 O O2' GDP . . . B 2 3.073 44.852 29.715 1 35.95 ? O2' GDP 2567 A 1 HETATM 17 C C1' GDP . . . B 2 1.365 46.101 28.653 1 30.5 ? C1' GDP 2567 A 1 HETATM 18 N N9 GDP . . . B 2 0.858 47.101 29.628 1 29.82 ? N9 GDP 2567 A 1 HETATM 19 C C8 GDP . . . B 2 -0.262 47.036 30.407 1 27.6 ? C8 GDP 2567 A 1 HETATM 20 N N7 GDP . . . B 2 -0.337 48.181 31.114 1 27.86 ? N7 GDP 2567 A 1 HETATM 21 C C5 GDP . . . B 2 0.722 48.953 30.8 1 27.19 ? C5 GDP 2567 A 1 HETATM 22 C C6 GDP . . . B 2 1.255 50.28 31.184 1 31.14 ? C6 GDP 2567 A 1 HETATM 23 O O6 GDP . . . B 2 0.603 50.929 32.064 1 29.7 ? O6 GDP 2567 A 1 HETATM 24 N N1 GDP . . . B 2 2.416 50.724 30.591 1 28.46 ? N1 GDP 2567 A 1 HETATM 25 C C2 GDP . . . B 2 3.061 49.997 29.67 1 28.45 ? C2 GDP 2567 A 1 HETATM 26 N N2 GDP . . . B 2 4.203 50.43 29.081 1 27.95 ? N2 GDP 2567 A 1 HETATM 27 N N3 GDP . . . B 2 2.617 48.772 29.306 1 29.79 ? N3 GDP 2567 A 1 HETATM 28 C C4 GDP . . . B 2 1.497 48.237 29.821 1 27.2 ? C4 GDP 2567 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #