data_1VG1 # _model_server_result.job_id 9SM8pqPCLYlgw3gjMwW2Yw _model_server_result.datetime_utc '2025-03-05 01:38:36' _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 1vg1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1557}' # _entry.id 1VG1 # _exptl.entry_id 1VG1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 1VG1 _cell.length_a 64.5 _cell.length_b 103.2 _cell.length_c 51.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VG1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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,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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OG1 THR 22 A THR 22 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc2 D O HOH . A HOH 1085 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc3 D O HOH . A HOH 1087 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 D O HOH . A HOH 1088 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 D O HOH . A HOH 1153 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 C O3B GDP . A GDP 1557 1_555 B MG MG . A MG 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? # _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 1VG1 _atom_sites.fract_transf_matrix[1][1] 0.015504 _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] 0.00969 _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] 0.019342 _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 MG A 1 3000 3000 MG MG2 . C 3 GDP A 1 1557 1557 GDP GDP . D 4 HOH A 1 1001 1001 HOH HOH . D 4 HOH A 2 1002 1002 HOH HOH . D 4 HOH A 3 1003 1003 HOH HOH . D 4 HOH A 4 1004 1004 HOH HOH . D 4 HOH A 5 1005 1005 HOH HOH . D 4 HOH A 6 1006 1006 HOH HOH . D 4 HOH A 7 1007 1007 HOH HOH . D 4 HOH A 8 1008 1008 HOH HOH . D 4 HOH A 9 1009 1009 HOH HOH . D 4 HOH A 10 1010 1010 HOH HOH . D 4 HOH A 11 1011 1011 HOH HOH . D 4 HOH A 12 1012 1012 HOH HOH . D 4 HOH A 13 1013 1013 HOH HOH . D 4 HOH A 14 1014 1014 HOH HOH . D 4 HOH A 15 1015 1015 HOH HOH . D 4 HOH A 16 1016 1016 HOH HOH . D 4 HOH A 17 1017 1017 HOH HOH . D 4 HOH A 18 1018 1018 HOH HOH . D 4 HOH A 19 1019 1019 HOH HOH . D 4 HOH A 20 1020 1020 HOH HOH . D 4 HOH A 21 1022 1022 HOH HOH . D 4 HOH A 22 1023 1023 HOH HOH . D 4 HOH A 23 1024 1024 HOH HOH . D 4 HOH A 24 1025 1025 HOH HOH . D 4 HOH A 25 1026 1026 HOH HOH . D 4 HOH A 26 1027 1027 HOH HOH . D 4 HOH A 27 1028 1028 HOH HOH . D 4 HOH A 28 1029 1029 HOH HOH . D 4 HOH A 29 1030 1030 HOH HOH . D 4 HOH A 30 1031 1031 HOH HOH . D 4 HOH A 31 1032 1032 HOH HOH . D 4 HOH A 32 1033 1033 HOH HOH . D 4 HOH A 33 1034 1034 HOH HOH . D 4 HOH A 34 1035 1035 HOH HOH . D 4 HOH A 35 1036 1036 HOH HOH . D 4 HOH A 36 1037 1037 HOH HOH . D 4 HOH A 37 1038 1038 HOH HOH . D 4 HOH A 38 1039 1039 HOH HOH . D 4 HOH A 39 1040 1040 HOH HOH . D 4 HOH A 40 1041 1041 HOH HOH . D 4 HOH A 41 1042 1042 HOH HOH . D 4 HOH A 42 1043 1043 HOH HOH . D 4 HOH A 43 1044 1044 HOH HOH . D 4 HOH A 44 1045 1045 HOH HOH . D 4 HOH A 45 1046 1046 HOH HOH . D 4 HOH A 46 1047 1047 HOH HOH . D 4 HOH A 47 1048 1048 HOH HOH . D 4 HOH A 48 1049 1049 HOH HOH . D 4 HOH A 49 1050 1050 HOH HOH . D 4 HOH A 50 1051 1051 HOH HOH . D 4 HOH A 51 1052 1052 HOH HOH . D 4 HOH A 52 1053 1053 HOH HOH . D 4 HOH A 53 1054 1054 HOH HOH . D 4 HOH A 54 1055 1055 HOH HOH . D 4 HOH A 55 1056 1056 HOH HOH . D 4 HOH A 56 1057 1057 HOH HOH . D 4 HOH A 57 1058 1058 HOH HOH . D 4 HOH A 58 1059 1059 HOH HOH . D 4 HOH A 59 1060 1060 HOH HOH . D 4 HOH A 60 1061 1061 HOH HOH . D 4 HOH A 61 1063 1063 HOH HOH . D 4 HOH A 62 1064 1064 HOH HOH . D 4 HOH A 63 1065 1065 HOH HOH . D 4 HOH A 64 1066 1066 HOH HOH . D 4 HOH A 65 1067 1067 HOH HOH . D 4 HOH A 66 1068 1068 HOH HOH . D 4 HOH A 67 1069 1069 HOH HOH . D 4 HOH A 68 1070 1070 HOH HOH . D 4 HOH A 69 1071 1071 HOH HOH . D 4 HOH A 70 1072 1072 HOH HOH . D 4 HOH A 71 1073 1073 HOH HOH . D 4 HOH A 72 1074 1074 HOH HOH . D 4 HOH A 73 1075 1075 HOH HOH . D 4 HOH A 74 1076 1076 HOH HOH . D 4 HOH A 75 1077 1077 HOH HOH . D 4 HOH A 76 1078 1078 HOH HOH . D 4 HOH A 77 1079 1079 HOH HOH . D 4 HOH A 78 1080 1080 HOH HOH . D 4 HOH A 79 1081 1081 HOH HOH . D 4 HOH A 80 1082 1082 HOH HOH . D 4 HOH A 81 1083 1083 HOH HOH . D 4 HOH A 82 1085 1085 HOH HOH . D 4 HOH A 83 1086 1086 HOH HOH . D 4 HOH A 84 1087 1087 HOH HOH . D 4 HOH A 85 1088 1088 HOH HOH . D 4 HOH A 86 1091 1091 HOH HOH . D 4 HOH A 87 1092 1092 HOH HOH . D 4 HOH A 88 1093 1093 HOH HOH . D 4 HOH A 89 1094 1094 HOH HOH . D 4 HOH A 90 1095 1095 HOH HOH . D 4 HOH A 91 1096 1096 HOH HOH . D 4 HOH A 92 1097 1097 HOH HOH . D 4 HOH A 93 1098 1098 HOH HOH . D 4 HOH A 94 1099 1099 HOH HOH . D 4 HOH A 95 1100 1100 HOH HOH . D 4 HOH A 96 1101 1101 HOH HOH . D 4 HOH A 97 1103 1103 HOH HOH . D 4 HOH A 98 1104 1104 HOH HOH . D 4 HOH A 99 1105 1105 HOH HOH . D 4 HOH A 100 1106 1106 HOH HOH . D 4 HOH A 101 1107 1107 HOH HOH . D 4 HOH A 102 1108 1108 HOH HOH . D 4 HOH A 103 1109 1109 HOH HOH . D 4 HOH A 104 1110 1110 HOH HOH . D 4 HOH A 105 1111 1111 HOH HOH . D 4 HOH A 106 1112 1112 HOH HOH . D 4 HOH A 107 1113 1113 HOH HOH . D 4 HOH A 108 1114 1114 HOH HOH . D 4 HOH A 109 1115 1115 HOH HOH . D 4 HOH A 110 1116 1116 HOH HOH . D 4 HOH A 111 1117 1117 HOH HOH . D 4 HOH A 112 1118 1118 HOH HOH . D 4 HOH A 113 1119 1119 HOH HOH . D 4 HOH A 114 1120 1120 HOH HOH . D 4 HOH A 115 1124 1124 HOH HOH . D 4 HOH A 116 1126 1126 HOH HOH . D 4 HOH A 117 1127 1127 HOH HOH . D 4 HOH A 118 1128 1128 HOH HOH . D 4 HOH A 119 1129 1129 HOH HOH . D 4 HOH A 120 1130 1130 HOH HOH . D 4 HOH A 121 1133 1133 HOH HOH . D 4 HOH A 122 1134 1134 HOH HOH . D 4 HOH A 123 1136 1136 HOH HOH . D 4 HOH A 124 1137 1137 HOH HOH . D 4 HOH A 125 1138 1138 HOH HOH . D 4 HOH A 126 1139 1139 HOH HOH . D 4 HOH A 127 1140 1140 HOH HOH . D 4 HOH A 128 1141 1141 HOH HOH . D 4 HOH A 129 1142 1142 HOH HOH . D 4 HOH A 130 1143 1143 HOH HOH . D 4 HOH A 131 1144 1144 HOH HOH . D 4 HOH A 132 1145 1145 HOH HOH . D 4 HOH A 133 1146 1146 HOH HOH . D 4 HOH A 134 1147 1147 HOH HOH . D 4 HOH A 135 1148 1148 HOH HOH . D 4 HOH A 136 1149 1149 HOH HOH . D 4 HOH A 137 1150 1150 HOH HOH . D 4 HOH A 138 1151 1151 HOH HOH . D 4 HOH A 139 1152 1152 HOH HOH . D 4 HOH A 140 1153 1153 HOH HOH . D 4 HOH A 141 1154 1154 HOH HOH . D 4 HOH A 142 1155 1155 HOH HOH . D 4 HOH A 143 1156 1156 HOH HOH . D 4 HOH A 144 1157 1157 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 . . . C 3 15.958 28.524 3.518 1 18.94 ? PB GDP 1557 A 1 HETATM 2 O O1B GDP . . . C 3 15.568 28.015 2.127 1 20.78 ? O1B GDP 1557 A 1 HETATM 3 O O2B GDP . . . C 3 16.538 29.901 3.522 1 18.64 ? O2B GDP 1557 A 1 HETATM 4 O O3B GDP . . . C 3 14.819 28.632 4.534 1 22.62 ? O3B GDP 1557 A 1 HETATM 5 O O3A GDP . . . C 3 17.263 27.72 4.277 1 22.28 ? O3A GDP 1557 A 1 HETATM 6 P PA GDP . . . C 3 17.197 26.156 4.737 1 22.4 ? PA GDP 1557 A 1 HETATM 7 O O1A GDP . . . C 3 17.227 26.419 6.231 1 19.85 ? O1A GDP 1557 A 1 HETATM 8 O O2A GDP . . . C 3 16.046 25.276 4.382 1 29.86 ? O2A GDP 1557 A 1 HETATM 9 O O5' GDP . . . C 3 18.661 25.752 4.325 1 19.27 ? O5' GDP 1557 A 1 HETATM 10 C C5' GDP . . . C 3 19.024 25.445 2.977 1 22.17 ? C5' GDP 1557 A 1 HETATM 11 C C4' GDP . . . C 3 20.077 24.358 3.011 1 19.39 ? C4' GDP 1557 A 1 HETATM 12 O O4' GDP . . . C 3 21.354 24.753 3.608 1 21.73 ? O4' GDP 1557 A 1 HETATM 13 C C3' GDP . . . C 3 19.713 23.086 3.839 1 23.76 ? C3' GDP 1557 A 1 HETATM 14 O O3' GDP . . . C 3 20.334 21.996 3.115 1 30.69 ? O3' GDP 1557 A 1 HETATM 15 C C2' GDP . . . C 3 20.389 23.294 5.196 1 19.12 ? C2' GDP 1557 A 1 HETATM 16 O O2' GDP . . . C 3 20.702 22.116 5.91 1 22.8 ? O2' GDP 1557 A 1 HETATM 17 C C1' GDP . . . C 3 21.607 24.088 4.842 1 21.31 ? C1' GDP 1557 A 1 HETATM 18 N N9 GDP . . . C 3 22.011 25.061 5.924 1 16.59 ? N9 GDP 1557 A 1 HETATM 19 C C8 GDP . . . C 3 21.297 25.971 6.684 1 15.18 ? C8 GDP 1557 A 1 HETATM 20 N N7 GDP . . . C 3 22.051 26.621 7.536 1 18.46 ? N7 GDP 1557 A 1 HETATM 21 C C5 GDP . . . C 3 23.328 26.133 7.358 1 15.89 ? C5 GDP 1557 A 1 HETATM 22 C C6 GDP . . . C 3 24.577 26.454 8.001 1 21.42 ? C6 GDP 1557 A 1 HETATM 23 O O6 GDP . . . C 3 24.752 27.29 8.91 1 19.93 ? O6 GDP 1557 A 1 HETATM 24 N N1 GDP . . . C 3 25.676 25.686 7.497 1 16.74 ? N1 GDP 1557 A 1 HETATM 25 C C2 GDP . . . C 3 25.578 24.736 6.492 1 26.4 ? C2 GDP 1557 A 1 HETATM 26 N N2 GDP . . . C 3 26.705 24.125 6.162 1 17.54 ? N2 GDP 1557 A 1 HETATM 27 N N3 GDP . . . C 3 24.391 24.42 5.866 1 18.5 ? N3 GDP 1557 A 1 HETATM 28 C C4 GDP . . . C 3 23.349 25.16 6.349 1 19.59 ? C4 GDP 1557 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #