data_2GJS # _model_server_result.job_id rt-NAT83scqCpn7OIgURqA _model_server_result.datetime_utc '2025-02-27 13:38:22' _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 2gjs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1184}' # _entry.id 2GJS # _exptl.entry_id 2GJS _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.18 _cell.angle_gamma 90 _cell.entry_id 2GJS _cell.length_a 51.427 _cell.length_b 58.56 _cell.length_c 53.603 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GJS _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 C MG MG . A MG 1 1_555 A OG SER 21 A SER 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc2 C MG MG . A MG 1 1_555 D O2B GDP . A GDP 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc3 C MG MG . A MG 1 1_555 G O HOH . A HOH 1186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc4 C MG MG . A MG 1 1_555 G O HOH . A HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 C MG MG . A MG 1 1_555 G O HOH . A HOH 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc6 C MG MG . A MG 1 1_555 G O HOH . A HOH 1211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc7 E MG MG . B MG 1 1_555 B OG SER 21 B SER 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc8 E MG MG . B MG 1 1_555 F O2B GDP . B GDP 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc9 E MG MG . B MG 1 1_555 H O HOH . B HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc10 E MG MG . B MG 1 1_555 H O HOH . B HOH 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc11 E MG MG . B MG 1 1_555 H O HOH . B HOH 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc12 E MG MG . B MG 1 1_555 H O HOH . B HOH 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? # _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 2GJS _atom_sites.fract_transf_matrix[1][1] 0.019445 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00245 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017077 _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] 0.018803 _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 C 2 MG A 1 1 1 MG MG . D 3 GDP A 1 1184 1184 GDP GDP . E 2 MG B 1 1 1 MG MG . F 3 GDP B 1 1184 1184 GDP GDP . G 4 HOH A 1 1185 8 HOH HOH . G 4 HOH A 2 1186 12 HOH HOH . G 4 HOH A 3 1187 13 HOH HOH . G 4 HOH A 4 1188 15 HOH HOH . G 4 HOH A 5 1189 17 HOH HOH . G 4 HOH A 6 1190 23 HOH HOH . G 4 HOH A 7 1191 24 HOH HOH . G 4 HOH A 8 1192 33 HOH HOH . G 4 HOH A 9 1193 34 HOH HOH . G 4 HOH A 10 1194 46 HOH HOH . G 4 HOH A 11 1195 50 HOH HOH . G 4 HOH A 12 1196 51 HOH HOH . G 4 HOH A 13 1197 52 HOH HOH . G 4 HOH A 14 1198 75 HOH HOH . G 4 HOH A 15 1199 76 HOH HOH . G 4 HOH A 16 1200 78 HOH HOH . G 4 HOH A 17 1201 81 HOH HOH . G 4 HOH A 18 1202 89 HOH HOH . G 4 HOH A 19 1203 100 HOH HOH . G 4 HOH A 20 1204 103 HOH HOH . G 4 HOH A 21 1205 104 HOH HOH . G 4 HOH A 22 1206 109 HOH HOH . G 4 HOH A 23 1207 113 HOH HOH . G 4 HOH A 24 1208 121 HOH HOH . G 4 HOH A 25 1209 135 HOH HOH . G 4 HOH A 26 1210 139 HOH HOH . G 4 HOH A 27 1211 143 HOH HOH . G 4 HOH A 28 1212 154 HOH HOH . G 4 HOH A 29 1213 155 HOH HOH . G 4 HOH A 30 1214 156 HOH HOH . G 4 HOH A 31 1215 157 HOH HOH . G 4 HOH A 32 1216 158 HOH HOH . G 4 HOH A 33 1217 159 HOH HOH . G 4 HOH A 34 1218 164 HOH HOH . G 4 HOH A 35 1219 165 HOH HOH . G 4 HOH A 36 1220 167 HOH HOH . G 4 HOH A 37 1221 170 HOH HOH . G 4 HOH A 38 1222 173 HOH HOH . G 4 HOH A 39 1223 174 HOH HOH . G 4 HOH A 40 1224 177 HOH HOH . G 4 HOH A 41 1225 181 HOH HOH . G 4 HOH A 42 1226 182 HOH HOH . G 4 HOH A 43 1227 183 HOH HOH . G 4 HOH A 44 1228 184 HOH HOH . G 4 HOH A 45 1229 185 HOH HOH . G 4 HOH A 46 1230 187 HOH HOH . G 4 HOH A 47 1231 188 HOH HOH . H 4 HOH B 1 1185 16 HOH HOH . H 4 HOH B 2 1186 18 HOH HOH . H 4 HOH B 3 1187 25 HOH HOH . H 4 HOH B 4 1188 35 HOH HOH . H 4 HOH B 5 1189 40 HOH HOH . H 4 HOH B 6 1190 43 HOH HOH . H 4 HOH B 7 1191 54 HOH HOH . H 4 HOH B 8 1192 59 HOH HOH . H 4 HOH B 9 1193 69 HOH HOH . H 4 HOH B 10 1194 82 HOH HOH . H 4 HOH B 11 1195 88 HOH HOH . H 4 HOH B 12 1196 94 HOH HOH . H 4 HOH B 13 1197 95 HOH HOH . H 4 HOH B 14 1198 115 HOH HOH . H 4 HOH B 15 1199 119 HOH HOH . H 4 HOH B 16 1200 132 HOH HOH . H 4 HOH B 17 1201 144 HOH HOH . H 4 HOH B 18 1202 146 HOH HOH . H 4 HOH B 19 1203 149 HOH HOH . H 4 HOH B 20 1204 150 HOH HOH . H 4 HOH B 21 1205 151 HOH HOH . H 4 HOH B 22 1206 160 HOH HOH . H 4 HOH B 23 1207 161 HOH HOH . H 4 HOH B 24 1208 162 HOH HOH . H 4 HOH B 25 1209 163 HOH HOH . H 4 HOH B 26 1210 166 HOH HOH . H 4 HOH B 27 1211 168 HOH HOH . H 4 HOH B 28 1212 175 HOH HOH . H 4 HOH B 29 1213 176 HOH HOH . H 4 HOH B 30 1214 178 HOH HOH . H 4 HOH B 31 1215 179 HOH HOH . H 4 HOH B 32 1216 180 HOH HOH . H 4 HOH B 33 1217 186 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 . . . D 3 41.219 34.595 24.383 1 27.26 ? PB GDP 1184 A 1 HETATM 2 O O1B GDP . . . D 3 39.905 35.278 24.27 1 27.83 ? O1B GDP 1184 A 1 HETATM 3 O O2B GDP . . . D 3 42.357 35.321 24.858 1 24.14 ? O2B GDP 1184 A 1 HETATM 4 O O3B GDP . . . D 3 41.592 34.031 23.007 1 23.99 ? O3B GDP 1184 A 1 HETATM 5 O O3A GDP . . . D 3 41.043 33.242 25.301 1 27.36 ? O3A GDP 1184 A 1 HETATM 6 P PA GDP . . . D 3 41.182 32.996 26.867 1 29.87 ? PA GDP 1184 A 1 HETATM 7 O O1A GDP . . . D 3 40.459 34.12 27.57 1 30.11 ? O1A GDP 1184 A 1 HETATM 8 O O2A GDP . . . D 3 42.623 32.865 27.193 1 26.98 ? O2A GDP 1184 A 1 HETATM 9 O O5' GDP . . . D 3 40.376 31.625 27.032 1 26.7 ? O5' GDP 1184 A 1 HETATM 10 C C5' GDP . . . D 3 39.016 31.585 26.782 1 25.41 ? C5' GDP 1184 A 1 HETATM 11 C C4' GDP . . . D 3 38.407 30.36 27.4 1 28.43 ? C4' GDP 1184 A 1 HETATM 12 O O4' GDP . . . D 3 39.097 29.191 26.963 1 29.7 ? O4' GDP 1184 A 1 HETATM 13 C C3' GDP . . . D 3 38.589 30.398 28.908 1 30.71 ? C3' GDP 1184 A 1 HETATM 14 O O3' GDP . . . D 3 37.399 29.776 29.426 1 31.28 ? O3' GDP 1184 A 1 HETATM 15 C C2' GDP . . . D 3 39.853 29.6 29.134 1 29.4 ? C2' GDP 1184 A 1 HETATM 16 O O2' GDP . . . D 3 39.995 28.919 30.391 1 30.72 ? O2' GDP 1184 A 1 HETATM 17 C C1' GDP . . . D 3 39.66 28.522 28.104 1 28.71 ? C1' GDP 1184 A 1 HETATM 18 N N9 GDP . . . D 3 40.834 27.842 27.569 1 28.96 ? N9 GDP 1184 A 1 HETATM 19 C C8 GDP . . . D 3 41.851 28.415 26.878 1 28.77 ? C8 GDP 1184 A 1 HETATM 20 N N7 GDP . . . D 3 42.706 27.477 26.462 1 29.1 ? N7 GDP 1184 A 1 HETATM 21 C C5 GDP . . . D 3 42.205 26.266 26.847 1 29.21 ? C5 GDP 1184 A 1 HETATM 22 C C6 GDP . . . D 3 42.632 24.853 26.658 1 27.04 ? C6 GDP 1184 A 1 HETATM 23 O O6 GDP . . . D 3 43.687 24.589 26.034 1 26.7 ? O6 GDP 1184 A 1 HETATM 24 N N1 GDP . . . D 3 41.867 23.912 27.235 1 28.71 ? N1 GDP 1184 A 1 HETATM 25 C C2 GDP . . . D 3 40.742 24.223 27.93 1 28.6 ? C2 GDP 1184 A 1 HETATM 26 N N2 GDP . . . D 3 40.034 23.235 28.478 1 29.29 ? N2 GDP 1184 A 1 HETATM 27 N N3 GDP . . . D 3 40.273 25.488 28.114 1 28.49 ? N3 GDP 1184 A 1 HETATM 28 C C4 GDP . . . D 3 40.972 26.524 27.577 1 29.7 ? C4 GDP 1184 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #