data_2GF9 # _model_server_result.job_id CiJT5JvrLORNlDQdmRkGYg _model_server_result.datetime_utc '2024-11-26 07:55:56' _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 2gf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 2GF9 # _exptl.entry_id 2GF9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 2GF9 _cell.length_a 35.7 _cell.length_b 63.222 _cell.length_c 67.695 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GF9 _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,D,E,F _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 4 _struct_asym.id E _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 36 A THR 36 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc2 B MG MG . A MG 201 1_555 E O1B GDP . A GDP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc3 B MG MG . A MG 201 1_555 F O HOH . A HOH 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc4 B MG MG . A MG 201 1_555 F O HOH . A HOH 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 B MG MG . A MG 201 1_555 F O HOH . A HOH 1054 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 B MG MG . A MG 201 1_555 F O HOH . A HOH 1056 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? # _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 2GF9 _atom_sites.fract_transf_matrix[1][1] 0.02801 _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] 0.01582 _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] 0.01477 _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 1 201 201 MG MG . C 3 UNX A 1 301 301 UNX UNX . D 3 UNX A 1 302 302 UNX UNX . E 4 GDP A 1 501 501 GDP GDP . F 5 HOH A 1 1001 1001 HOH HOH . F 5 HOH A 2 1002 1002 HOH HOH . F 5 HOH A 3 1003 1003 HOH HOH . F 5 HOH A 4 1004 1004 HOH HOH . F 5 HOH A 5 1005 1005 HOH HOH . F 5 HOH A 6 1006 1006 HOH HOH . F 5 HOH A 7 1007 1007 HOH HOH . F 5 HOH A 8 1008 1008 HOH HOH . F 5 HOH A 9 1009 1009 HOH HOH . F 5 HOH A 10 1010 1010 HOH HOH . F 5 HOH A 11 1011 1011 HOH HOH . F 5 HOH A 12 1012 1012 HOH HOH . F 5 HOH A 13 1013 1013 HOH HOH . F 5 HOH A 14 1014 1014 HOH HOH . F 5 HOH A 15 1015 1015 HOH HOH . F 5 HOH A 16 1016 1016 HOH HOH . F 5 HOH A 17 1017 1017 HOH HOH . F 5 HOH A 18 1018 1018 HOH HOH . F 5 HOH A 19 1019 1019 HOH HOH . F 5 HOH A 20 1020 1020 HOH HOH . F 5 HOH A 21 1021 1021 HOH HOH . F 5 HOH A 22 1022 1022 HOH HOH . F 5 HOH A 23 1023 1023 HOH HOH . F 5 HOH A 24 1024 1024 HOH HOH . F 5 HOH A 25 1025 1025 HOH HOH . F 5 HOH A 26 1026 1026 HOH HOH . F 5 HOH A 27 1027 1027 HOH HOH . F 5 HOH A 28 1028 1028 HOH HOH . F 5 HOH A 29 1029 1029 HOH HOH . F 5 HOH A 30 1030 1030 HOH HOH . F 5 HOH A 31 1031 1031 HOH HOH . F 5 HOH A 32 1032 1032 HOH HOH . F 5 HOH A 33 1033 1033 HOH HOH . F 5 HOH A 34 1034 1034 HOH HOH . F 5 HOH A 35 1035 1035 HOH HOH . F 5 HOH A 36 1036 1036 HOH HOH . F 5 HOH A 37 1037 1037 HOH HOH . F 5 HOH A 38 1038 1038 HOH HOH . F 5 HOH A 39 1039 1039 HOH HOH . F 5 HOH A 40 1040 1040 HOH HOH . F 5 HOH A 41 1041 1041 HOH HOH . F 5 HOH A 42 1042 1042 HOH HOH . F 5 HOH A 43 1043 1043 HOH HOH . F 5 HOH A 44 1044 1044 HOH HOH . F 5 HOH A 45 1045 1045 HOH HOH . F 5 HOH A 46 1046 1046 HOH HOH . F 5 HOH A 47 1047 1047 HOH HOH . F 5 HOH A 48 1048 1048 HOH HOH . F 5 HOH A 49 1049 1049 HOH HOH . F 5 HOH A 50 1050 1050 HOH HOH . F 5 HOH A 51 1051 1051 HOH HOH . F 5 HOH A 52 1052 1052 HOH HOH . F 5 HOH A 53 1053 1053 HOH HOH . F 5 HOH A 54 1054 1054 HOH HOH . F 5 HOH A 55 1055 1055 HOH HOH . F 5 HOH A 56 1056 1056 HOH HOH . F 5 HOH A 57 1057 1057 HOH HOH . F 5 HOH A 58 1058 1058 HOH HOH . F 5 HOH A 59 1059 1059 HOH HOH . F 5 HOH A 60 1060 1060 HOH HOH . F 5 HOH A 61 1061 1061 HOH HOH . F 5 HOH A 62 1062 1062 HOH HOH . F 5 HOH A 63 1063 1063 HOH HOH . F 5 HOH A 64 1064 1064 HOH HOH . F 5 HOH A 65 1065 1065 HOH HOH . F 5 HOH A 66 1066 1066 HOH HOH . F 5 HOH A 67 1067 1067 HOH HOH . F 5 HOH A 68 1068 1068 HOH HOH . F 5 HOH A 69 1069 1069 HOH HOH . F 5 HOH A 70 1070 1070 HOH HOH . F 5 HOH A 71 1071 1071 HOH HOH . F 5 HOH A 72 1072 1072 HOH HOH . F 5 HOH A 73 1073 1073 HOH HOH . F 5 HOH A 74 1074 1074 HOH HOH . F 5 HOH A 75 1075 1075 HOH HOH . F 5 HOH A 76 1076 1076 HOH HOH . F 5 HOH A 77 1077 1077 HOH HOH . F 5 HOH A 78 1078 1078 HOH HOH . F 5 HOH A 79 1079 1079 HOH HOH . F 5 HOH A 80 1080 1080 HOH HOH . F 5 HOH A 81 1081 1081 HOH HOH . F 5 HOH A 82 1082 1082 HOH HOH . F 5 HOH A 83 1083 1083 HOH HOH . F 5 HOH A 84 1084 1084 HOH HOH . F 5 HOH A 85 1085 1085 HOH HOH . F 5 HOH A 86 1086 1086 HOH HOH . F 5 HOH A 87 1087 1087 HOH HOH . F 5 HOH A 88 1088 1088 HOH HOH . F 5 HOH A 89 1089 1089 HOH HOH . F 5 HOH A 90 1090 1090 HOH HOH . F 5 HOH A 91 1091 1091 HOH HOH . F 5 HOH A 92 1092 1092 HOH HOH . F 5 HOH A 93 1093 1093 HOH HOH . F 5 HOH A 94 1094 1094 HOH HOH . F 5 HOH A 95 1095 1095 HOH HOH . F 5 HOH A 96 1096 1096 HOH HOH . F 5 HOH A 97 1097 1097 HOH HOH . F 5 HOH A 98 1098 1098 HOH HOH . F 5 HOH A 99 1099 1099 HOH HOH . F 5 HOH A 100 1100 1100 HOH HOH . F 5 HOH A 101 1101 1101 HOH HOH . F 5 HOH A 102 1102 1102 HOH HOH . F 5 HOH A 103 1103 1103 HOH HOH . F 5 HOH A 104 1104 1104 HOH HOH . F 5 HOH A 105 1105 1105 HOH HOH . F 5 HOH A 106 1106 1106 HOH HOH . F 5 HOH A 107 1107 1107 HOH HOH . F 5 HOH A 108 1108 1108 HOH HOH . F 5 HOH A 109 1109 1109 HOH HOH . F 5 HOH A 110 1110 1110 HOH HOH . F 5 HOH A 111 1111 1111 HOH HOH . F 5 HOH A 112 1112 1112 HOH HOH . F 5 HOH A 113 1113 1113 HOH HOH . F 5 HOH A 114 1114 1114 HOH HOH . F 5 HOH A 115 1115 1115 HOH HOH . F 5 HOH A 116 1116 1116 HOH HOH . F 5 HOH A 117 1117 1117 HOH HOH . F 5 HOH A 118 1118 1118 HOH HOH . F 5 HOH A 119 1119 1119 HOH HOH . F 5 HOH A 120 1120 1120 HOH HOH . F 5 HOH A 121 1121 1121 HOH HOH . F 5 HOH A 122 1122 1122 HOH HOH . F 5 HOH A 123 1123 1123 HOH HOH . F 5 HOH A 124 1124 1124 HOH HOH . F 5 HOH A 125 1125 1125 HOH HOH . F 5 HOH A 126 1126 1126 HOH HOH . F 5 HOH A 127 1127 1127 HOH HOH . F 5 HOH A 128 1128 1128 HOH HOH . F 5 HOH A 129 1129 1129 HOH HOH . F 5 HOH A 130 1130 1130 HOH HOH . F 5 HOH A 131 1131 1131 HOH HOH . F 5 HOH A 132 1132 1132 HOH HOH . F 5 HOH A 133 1133 1133 HOH HOH . F 5 HOH A 134 1134 1134 HOH HOH . F 5 HOH A 135 1135 1135 HOH HOH . F 5 HOH A 136 1136 1136 HOH HOH . F 5 HOH A 137 1137 1137 HOH HOH . F 5 HOH A 138 1138 1138 HOH HOH . F 5 HOH A 139 1139 1139 HOH HOH . F 5 HOH A 140 1140 1140 HOH HOH . F 5 HOH A 141 1141 1141 HOH HOH . F 5 HOH A 142 1142 1142 HOH HOH . F 5 HOH A 143 1143 1143 HOH HOH . F 5 HOH A 144 1144 1144 HOH HOH . F 5 HOH A 145 1145 1145 HOH HOH . F 5 HOH A 146 1146 1146 HOH HOH . F 5 HOH A 147 1147 1147 HOH HOH . F 5 HOH A 148 1148 1148 HOH HOH . F 5 HOH A 149 1149 1149 HOH HOH . F 5 HOH A 150 1150 1150 HOH HOH . F 5 HOH A 151 1151 1151 HOH HOH . F 5 HOH A 152 1152 1152 HOH HOH . F 5 HOH A 153 1153 1153 HOH HOH . F 5 HOH A 154 1154 1154 HOH HOH . F 5 HOH A 155 1155 1155 HOH HOH . F 5 HOH A 156 1156 1156 HOH HOH . F 5 HOH A 157 1157 1157 HOH HOH . F 5 HOH A 158 1158 1158 HOH HOH . F 5 HOH A 159 1159 1159 HOH HOH . F 5 HOH A 160 1160 1160 HOH HOH . F 5 HOH A 161 1161 1161 HOH HOH . F 5 HOH A 162 1162 1162 HOH HOH . F 5 HOH A 163 1163 1163 HOH HOH . F 5 HOH A 164 1164 1164 HOH HOH . F 5 HOH A 165 1165 1165 HOH HOH . F 5 HOH A 166 1166 1166 HOH HOH . F 5 HOH A 167 1167 1167 HOH HOH . F 5 HOH A 168 1168 1168 HOH HOH . F 5 HOH A 169 1169 1169 HOH HOH . F 5 HOH A 170 1170 1170 HOH HOH . F 5 HOH A 171 1171 1171 HOH HOH . F 5 HOH A 172 1172 1172 HOH HOH . F 5 HOH A 173 1173 1173 HOH HOH . F 5 HOH A 174 1174 1174 HOH HOH . F 5 HOH A 175 1175 1175 HOH HOH . F 5 HOH A 176 1176 1176 HOH HOH . F 5 HOH A 177 1177 1177 HOH HOH . F 5 HOH A 178 1178 1178 HOH HOH . F 5 HOH A 179 1179 1179 HOH HOH . F 5 HOH A 180 1180 1180 HOH HOH . F 5 HOH A 181 1181 1181 HOH HOH . F 5 HOH A 182 1182 1182 HOH HOH . F 5 HOH A 183 1183 1183 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 . . . E 4 1.072 13.197 11.186 1 5.44 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . E 4 1.197 12.382 12.464 1 5.07 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . E 4 -0.345 13.657 10.866 1 5.65 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . E 4 2.095 14.324 11.076 1 5.19 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . E 4 1.504 12.181 9.973 1 4.11 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . E 4 1.455 10.581 9.955 1 5.27 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . E 4 2.664 9.998 10.606 1 5.94 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . E 4 0.117 10.083 10.407 1 6.53 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . E 4 1.688 10.343 8.383 1 4.83 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . E 4 0.782 10.923 7.419 1 5.47 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . E 4 0.825 10.141 6.116 1 6.3 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . E 4 2.127 10.321 5.549 1 5.15 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . E 4 0.628 8.64 6.293 1 5.48 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . E 4 -0.041 8.119 5.121 1 5.5 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . E 4 2.038 8.117 6.375 1 3.59 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . E 4 2.197 6.753 5.997 1 6.64 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . E 4 2.744 9.038 5.405 1 4.71 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . E 4 4.164 9.169 5.678 1 4.5 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . E 4 4.769 9.4 6.892 1 5.62 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . E 4 6.11 9.496 6.746 1 5.01 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . E 4 6.356 9.313 5.42 1 5.13 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . E 4 7.544 9.283 4.584 1 5.7 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . E 4 8.711 9.448 5.061 1 5.18 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . E 4 7.36 9.082 3.263 1 4.28 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . E 4 6.142 8.91 2.68 1 4.33 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . E 4 6.072 8.719 1.358 1 5.29 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . E 4 5.001 8.904 3.413 1 5.88 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . E 4 5.074 9.108 4.74 1 4.54 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 28 #