data_2G3Y # _model_server_result.job_id bH6L48gySVvEKDXiVJx6ag _model_server_result.datetime_utc '2025-02-27 14:06:27' _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 2g3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 2G3Y # _exptl.entry_id 2G3Y _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 2G3Y _cell.length_a 51.242 _cell.length_b 51.242 _cell.length_c 173.873 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2G3Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 2G3Y _atom_sites.fract_transf_matrix[1][1] 0.019515 _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] 0.019515 _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] 0.005751 _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 1001 1001 GDP GDP . C 3 HOH A 1 1002 1 HOH HOH . C 3 HOH A 2 1003 2 HOH HOH . C 3 HOH A 3 1004 3 HOH HOH . C 3 HOH A 4 1005 4 HOH HOH . C 3 HOH A 5 1006 6 HOH HOH . C 3 HOH A 6 1007 10 HOH HOH . C 3 HOH A 7 1008 12 HOH HOH . C 3 HOH A 8 1009 13 HOH HOH . C 3 HOH A 9 1010 15 HOH HOH . C 3 HOH A 10 1011 18 HOH HOH . C 3 HOH A 11 1012 19 HOH HOH . C 3 HOH A 12 1013 20 HOH HOH . C 3 HOH A 13 1014 21 HOH HOH . C 3 HOH A 14 1015 24 HOH HOH . C 3 HOH A 15 1016 26 HOH HOH . C 3 HOH A 16 1017 27 HOH HOH . C 3 HOH A 17 1018 28 HOH HOH . C 3 HOH A 18 1019 30 HOH HOH . C 3 HOH A 19 1020 32 HOH HOH . C 3 HOH A 20 1021 33 HOH HOH . C 3 HOH A 21 1022 35 HOH HOH . C 3 HOH A 22 1023 38 HOH HOH . C 3 HOH A 23 1024 41 HOH HOH . C 3 HOH A 24 1025 42 HOH HOH . C 3 HOH A 25 1026 43 HOH HOH . C 3 HOH A 26 1027 48 HOH HOH . C 3 HOH A 27 1028 49 HOH HOH . C 3 HOH A 28 1029 54 HOH HOH . C 3 HOH A 29 1030 56 HOH HOH . C 3 HOH A 30 1031 62 HOH HOH . C 3 HOH A 31 1032 64 HOH HOH . C 3 HOH A 32 1033 65 HOH HOH . C 3 HOH A 33 1034 69 HOH HOH . C 3 HOH A 34 1035 73 HOH HOH . C 3 HOH A 35 1036 79 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 -17.231 6.42 -10.737 1 39.61 ? PB GDP 1001 A 1 HETATM 2 O O1B GDP . . . B 2 -15.799 6.096 -10.428 1 39.77 ? O1B GDP 1001 A 1 HETATM 3 O O2B GDP . . . B 2 -17.596 5.97 -12.138 1 38.53 ? O2B GDP 1001 A 1 HETATM 4 O O3B GDP . . . B 2 -18.178 5.817 -9.745 1 39.84 ? O3B GDP 1001 A 1 HETATM 5 O O3A GDP . . . B 2 -17.317 8.019 -10.566 1 44.03 ? O3A GDP 1001 A 1 HETATM 6 P PA GDP . . . B 2 -18.258 9.034 -11.4 1 43.19 ? PA GDP 1001 A 1 HETATM 7 O O1A GDP . . . B 2 -19.675 8.543 -11.328 1 43.21 ? O1A GDP 1001 A 1 HETATM 8 O O2A GDP . . . B 2 -17.707 9.295 -12.783 1 41.02 ? O2A GDP 1001 A 1 HETATM 9 O O5' GDP . . . B 2 -18.055 10.318 -10.472 1 45.34 ? O5' GDP 1001 A 1 HETATM 10 C C5' GDP . . . B 2 -18.724 10.421 -9.21 1 45.07 ? C5' GDP 1001 A 1 HETATM 11 C C4' GDP . . . B 2 -18.866 11.902 -8.902 1 45.61 ? C4' GDP 1001 A 1 HETATM 12 O O4' GDP . . . B 2 -17.587 12.531 -8.997 1 45 ? O4' GDP 1001 A 1 HETATM 13 C C3' GDP . . . B 2 -19.752 12.588 -9.938 1 45.71 ? C3' GDP 1001 A 1 HETATM 14 O O3' GDP . . . B 2 -20.596 13.517 -9.27 1 47.21 ? O3' GDP 1001 A 1 HETATM 15 C C2' GDP . . . B 2 -18.791 13.272 -10.883 1 44.18 ? C2' GDP 1001 A 1 HETATM 16 O O2' GDP . . . B 2 -19.299 14.476 -11.444 1 45.26 ? O2' GDP 1001 A 1 HETATM 17 C C1' GDP . . . B 2 -17.637 13.584 -9.968 1 42.73 ? C1' GDP 1001 A 1 HETATM 18 N N9 GDP . . . B 2 -16.345 13.701 -10.669 1 41.84 ? N9 GDP 1001 A 1 HETATM 19 C C8 GDP . . . B 2 -15.735 12.829 -11.489 1 42.46 ? C8 GDP 1001 A 1 HETATM 20 N N7 GDP . . . B 2 -14.541 13.327 -11.921 1 41.92 ? N7 GDP 1001 A 1 HETATM 21 C C5 GDP . . . B 2 -14.387 14.536 -11.362 1 40.77 ? C5 GDP 1001 A 1 HETATM 22 C C6 GDP . . . B 2 -13.377 15.6 -11.355 1 41.5 ? C6 GDP 1001 A 1 HETATM 23 O O6 GDP . . . B 2 -12.314 15.517 -12.01 1 41.74 ? O6 GDP 1001 A 1 HETATM 24 N N1 GDP . . . B 2 -13.64 16.691 -10.616 1 42.85 ? N1 GDP 1001 A 1 HETATM 25 C C2 GDP . . . B 2 -14.763 16.831 -9.902 1 41.87 ? C2 GDP 1001 A 1 HETATM 26 N N2 GDP . . . B 2 -14.984 17.927 -9.178 1 42.75 ? N2 GDP 1001 A 1 HETATM 27 N N3 GDP . . . B 2 -15.724 15.902 -9.849 1 43.58 ? N3 GDP 1001 A 1 HETATM 28 C C4 GDP . . . B 2 -15.577 14.755 -10.547 1 41.85 ? C4 GDP 1001 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 1181 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #