data_3T12 # _model_server_result.job_id RoLGpH2mHH1NbpYoInHgng _model_server_result.datetime_utc '2024-11-22 19:12:14' _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 3t12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":197}' # _entry.id 3T12 # _exptl.entry_id 3T12 _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 3T12 _cell.length_a 106.5 _cell.length_b 174.2 _cell.length_c 69.2 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T12 _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 PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 D _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 28 A THR 26 1_555 E MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc2 A OG1 THR 56 A THR 54 1_555 E MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc3 D O2B GDP . A GDP 197 1_555 E MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc4 E MG MG . A MG 198 1_555 I O HOH . A HOH 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc5 E MG MG . A MG 198 1_555 I O HOH . A HOH 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc6 E MG MG . A MG 198 1_555 I O HOH . A HOH 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? # _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 74 n n PB O2B GDP sing 75 n n PB O3B GDP sing 76 n n PB O3A GDP sing 77 n n O2B HOB2 GDP sing 78 n n O3B HOB3 GDP sing 79 n n O3A PA GDP sing 80 n n PA O1A GDP doub 81 n n PA O2A GDP sing 82 n n PA O5' GDP sing 83 n n O2A HOA2 GDP sing 84 n n O5' C5' GDP sing 85 n n C5' C4' GDP sing 86 n n C5' H5' GDP sing 87 n n C5' "H5''" GDP sing 88 n n C4' O4' GDP sing 89 n n C4' C3' GDP sing 90 n n C4' H4' GDP sing 91 n n O4' C1' GDP sing 92 n n C3' O3' GDP sing 93 n n C3' C2' GDP sing 94 n n C3' H3' GDP sing 95 n n O3' HO3' GDP sing 96 n n C2' O2' GDP sing 97 n n C2' C1' GDP sing 98 n n C2' H2' GDP sing 99 n n O2' HO2' GDP sing 100 n n C1' N9 GDP sing 101 n n C1' H1' GDP sing 102 n n N9 C8 GDP sing 103 n y N9 C4 GDP sing 104 n y C8 N7 GDP doub 105 n y C8 H8 GDP sing 106 n n N7 C5 GDP sing 107 n y C5 C6 GDP sing 108 n n C5 C4 GDP doub 109 n y C6 O6 GDP doub 110 n n C6 N1 GDP sing 111 n n N1 C2 GDP sing 112 n n N1 HN1 GDP sing 113 n n C2 N2 GDP sing 114 n n C2 N3 GDP doub 115 n n N2 HN21 GDP sing 116 n n N2 HN22 GDP sing 117 n n N3 C4 GDP sing 118 n n # _atom_sites.entry_id 3T12 _atom_sites.fract_transf_matrix[1][1] 0.00939 _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] 0.005741 _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] 0.014451 _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 D 3 GDP A 1 197 167 GDP GDP . E 4 MG A 1 198 1 MG MG . F 4 MG A 1 199 1 MG MG . G 5 ALF A 1 200 3 ALF ALF . H 4 MG B 1 1 1 MG MG . I 6 HOH A 1 201 2 HOH HOH . I 6 HOH A 2 202 3 HOH HOH . I 6 HOH A 3 203 4 HOH HOH . I 6 HOH A 4 204 5 HOH HOH . I 6 HOH A 5 205 6 HOH HOH . I 6 HOH A 6 206 7 HOH HOH . I 6 HOH A 7 207 8 HOH HOH . I 6 HOH A 8 208 9 HOH HOH . I 6 HOH A 9 209 10 HOH HOH . I 6 HOH A 10 210 14 HOH HOH . I 6 HOH A 11 211 211 HOH HOH . I 6 HOH A 12 212 20 HOH HOH . I 6 HOH A 13 213 213 HOH HOH . I 6 HOH A 14 214 21 HOH HOH . I 6 HOH A 15 215 24 HOH HOH . I 6 HOH A 16 216 26 HOH HOH . I 6 HOH A 17 217 34 HOH HOH . I 6 HOH A 18 218 35 HOH HOH . I 6 HOH A 19 219 40 HOH HOH . I 6 HOH A 20 220 43 HOH HOH . I 6 HOH A 21 221 46 HOH HOH . I 6 HOH A 22 222 50 HOH HOH . I 6 HOH A 23 223 52 HOH HOH . I 6 HOH A 24 224 224 HOH HOH . I 6 HOH A 25 225 53 HOH HOH . I 6 HOH A 26 226 56 HOH HOH . I 6 HOH A 27 227 57 HOH HOH . I 6 HOH A 28 228 59 HOH HOH . I 6 HOH A 29 229 63 HOH HOH . I 6 HOH A 30 230 64 HOH HOH . I 6 HOH A 31 231 76 HOH HOH . I 6 HOH A 32 232 87 HOH HOH . I 6 HOH A 33 233 88 HOH HOH . I 6 HOH A 34 234 89 HOH HOH . I 6 HOH A 35 235 90 HOH HOH . I 6 HOH A 36 236 91 HOH HOH . I 6 HOH A 37 237 92 HOH HOH . I 6 HOH A 38 238 95 HOH HOH . I 6 HOH A 39 239 105 HOH HOH . I 6 HOH A 40 240 106 HOH HOH . I 6 HOH A 41 241 107 HOH HOH . I 6 HOH A 42 242 242 HOH HOH . I 6 HOH A 43 243 243 HOH HOH . I 6 HOH A 44 244 109 HOH HOH . I 6 HOH A 45 245 110 HOH HOH . I 6 HOH A 46 246 246 HOH HOH . I 6 HOH A 47 247 111 HOH HOH . I 6 HOH A 48 248 112 HOH HOH . I 6 HOH A 49 249 121 HOH HOH . I 6 HOH A 50 250 127 HOH HOH . I 6 HOH A 51 251 139 HOH HOH . I 6 HOH A 52 252 140 HOH HOH . I 6 HOH A 53 253 144 HOH HOH . I 6 HOH A 54 254 158 HOH HOH . I 6 HOH A 55 255 255 HOH HOH . I 6 HOH A 56 256 256 HOH HOH . I 6 HOH A 57 257 160 HOH HOH . I 6 HOH A 58 258 168 HOH HOH . I 6 HOH A 59 259 169 HOH HOH . I 6 HOH A 60 260 172 HOH HOH . I 6 HOH A 61 261 174 HOH HOH . I 6 HOH A 62 262 175 HOH HOH . I 6 HOH A 63 263 176 HOH HOH . I 6 HOH A 64 264 187 HOH HOH . I 6 HOH A 65 265 189 HOH HOH . I 6 HOH A 66 266 266 HOH HOH . I 6 HOH A 67 267 267 HOH HOH . I 6 HOH A 68 268 268 HOH HOH . I 6 HOH A 69 269 190 HOH HOH . I 6 HOH A 70 270 192 HOH HOH . I 6 HOH A 71 271 195 HOH HOH . I 6 HOH A 72 272 200 HOH HOH . I 6 HOH A 73 273 66 HOH HOH . I 6 HOH A 74 278 278 HOH HOH . I 6 HOH A 75 280 280 HOH HOH . I 6 HOH A 76 281 281 HOH HOH . J 6 HOH B 1 140 11 HOH HOH . J 6 HOH B 2 141 18 HOH HOH . J 6 HOH B 3 142 142 HOH HOH . J 6 HOH B 4 143 19 HOH HOH . J 6 HOH B 5 144 23 HOH HOH . J 6 HOH B 6 145 25 HOH HOH . J 6 HOH B 7 146 146 HOH HOH . J 6 HOH B 8 147 30 HOH HOH . J 6 HOH B 9 148 148 HOH HOH . J 6 HOH B 10 149 33 HOH HOH . J 6 HOH B 11 150 38 HOH HOH . J 6 HOH B 12 151 151 HOH HOH . J 6 HOH B 13 152 152 HOH HOH . J 6 HOH B 14 153 45 HOH HOH . J 6 HOH B 15 154 55 HOH HOH . J 6 HOH B 16 155 155 HOH HOH . J 6 HOH B 17 156 58 HOH HOH . J 6 HOH B 18 157 61 HOH HOH . J 6 HOH B 19 158 65 HOH HOH . J 6 HOH B 20 160 67 HOH HOH . J 6 HOH B 21 161 68 HOH HOH . J 6 HOH B 22 162 71 HOH HOH . J 6 HOH B 23 163 163 HOH HOH . J 6 HOH B 24 164 74 HOH HOH . J 6 HOH B 25 165 75 HOH HOH . J 6 HOH B 26 166 77 HOH HOH . J 6 HOH B 27 167 93 HOH HOH . J 6 HOH B 28 168 96 HOH HOH . J 6 HOH B 29 169 98 HOH HOH . J 6 HOH B 30 170 114 HOH HOH . J 6 HOH B 31 171 117 HOH HOH . J 6 HOH B 32 172 122 HOH HOH . J 6 HOH B 33 173 173 HOH HOH . J 6 HOH B 34 174 125 HOH HOH . J 6 HOH B 35 175 130 HOH HOH . J 6 HOH B 36 176 133 HOH HOH . J 6 HOH B 37 177 135 HOH HOH . J 6 HOH B 38 179 179 HOH HOH . J 6 HOH B 39 188 188 HOH HOH . J 6 HOH B 40 194 194 HOH HOH . J 6 HOH B 41 203 203 HOH HOH . J 6 HOH B 42 209 209 HOH HOH . J 6 HOH B 43 229 229 HOH HOH . J 6 HOH B 44 235 235 HOH HOH . J 6 HOH B 45 253 253 HOH HOH . J 6 HOH B 46 254 254 HOH HOH . J 6 HOH B 47 258 258 HOH HOH . J 6 HOH B 48 259 259 HOH HOH . J 6 HOH B 49 261 261 HOH HOH . J 6 HOH B 50 264 264 HOH HOH . J 6 HOH B 51 269 269 HOH HOH . J 6 HOH B 52 270 270 HOH HOH . J 6 HOH B 53 273 273 HOH HOH . J 6 HOH B 54 274 274 HOH HOH . J 6 HOH B 55 275 275 HOH HOH . J 6 HOH B 56 276 276 HOH HOH . J 6 HOH B 57 279 279 HOH HOH . J 6 HOH B 58 282 282 HOH HOH . J 6 HOH B 59 285 285 HOH HOH . J 6 HOH B 60 286 286 HOH HOH . K 6 HOH C 1 140 16 HOH HOH . K 6 HOH C 2 141 141 HOH HOH . K 6 HOH C 3 142 17 HOH HOH . K 6 HOH C 4 143 22 HOH HOH . K 6 HOH C 5 144 29 HOH HOH . K 6 HOH C 6 145 31 HOH HOH . K 6 HOH C 7 146 32 HOH HOH . K 6 HOH C 8 147 147 HOH HOH . K 6 HOH C 9 148 36 HOH HOH . K 6 HOH C 10 149 37 HOH HOH . K 6 HOH C 11 150 41 HOH HOH . K 6 HOH C 12 151 44 HOH HOH . K 6 HOH C 13 152 48 HOH HOH . K 6 HOH C 14 153 49 HOH HOH . K 6 HOH C 15 154 154 HOH HOH . K 6 HOH C 16 155 54 HOH HOH . K 6 HOH C 17 156 156 HOH HOH . K 6 HOH C 18 157 79 HOH HOH . K 6 HOH C 19 158 80 HOH HOH . K 6 HOH C 20 159 159 HOH HOH . K 6 HOH C 21 160 81 HOH HOH . K 6 HOH C 22 161 82 HOH HOH . K 6 HOH C 23 162 162 HOH HOH . K 6 HOH C 24 163 85 HOH HOH . K 6 HOH C 25 164 164 HOH HOH . K 6 HOH C 26 165 86 HOH HOH . K 6 HOH C 27 166 100 HOH HOH . K 6 HOH C 28 167 101 HOH HOH . K 6 HOH C 29 168 102 HOH HOH . K 6 HOH C 30 169 103 HOH HOH . K 6 HOH C 31 170 170 HOH HOH . K 6 HOH C 32 171 104 HOH HOH . K 6 HOH C 33 172 115 HOH HOH . K 6 HOH C 34 173 120 HOH HOH . K 6 HOH C 35 174 126 HOH HOH . K 6 HOH C 36 175 132 HOH HOH . K 6 HOH C 37 176 136 HOH HOH . K 6 HOH C 38 180 180 HOH HOH . K 6 HOH C 39 184 184 HOH HOH . K 6 HOH C 40 185 185 HOH HOH . K 6 HOH C 41 186 186 HOH HOH . K 6 HOH C 42 204 204 HOH HOH . K 6 HOH C 43 205 205 HOH HOH . K 6 HOH C 44 206 206 HOH HOH . K 6 HOH C 45 208 208 HOH HOH . K 6 HOH C 46 225 225 HOH HOH . K 6 HOH C 47 228 228 HOH HOH . K 6 HOH C 48 234 234 HOH HOH . K 6 HOH C 49 236 236 HOH HOH . K 6 HOH C 50 257 257 HOH HOH . K 6 HOH C 51 265 265 HOH HOH . K 6 HOH C 52 272 272 HOH HOH . K 6 HOH C 53 277 277 HOH HOH . K 6 HOH C 54 283 283 HOH HOH . K 6 HOH C 55 284 284 HOH HOH . K 6 HOH C 56 287 287 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 34.846 18.815 -3.969 1 25.91 ? PB GDP 197 A 1 HETATM 2 O O1B GDP . . . D 3 34.13 18.852 -5.271 1 22.04 ? O1B GDP 197 A 1 HETATM 3 O O2B GDP . . . D 3 34.441 19.997 -3.123 1 20.78 ? O2B GDP 197 A 1 HETATM 4 O O3B GDP . . . D 3 34.534 17.491 -3.241 1 23.55 ? O3B GDP 197 A 1 HETATM 5 O O3A GDP . . . D 3 36.376 18.944 -4.352 1 24.97 ? O3A GDP 197 A 1 HETATM 6 P PA GDP . . . D 3 37.244 20.234 -3.917 1 28.43 ? PA GDP 197 A 1 HETATM 7 O O1A GDP . . . D 3 36.535 21.46 -4.502 1 26.54 ? O1A GDP 197 A 1 HETATM 8 O O2A GDP . . . D 3 37.467 20.092 -2.441 1 25.48 ? O2A GDP 197 A 1 HETATM 9 O O5' GDP . . . D 3 38.589 19.771 -4.674 1 30.99 ? O5' GDP 197 A 1 HETATM 10 C C5' GDP . . . D 3 39.074 18.42 -4.527 1 31.65 ? C5' GDP 197 A 1 HETATM 11 C C4' GDP . . . D 3 40.532 18.397 -4.941 1 33.01 ? C4' GDP 197 A 1 HETATM 12 O O4' GDP . . . D 3 40.571 18.595 -6.366 1 32.57 ? O4' GDP 197 A 1 HETATM 13 C C3' GDP . . . D 3 41.299 19.536 -4.275 1 31.44 ? C3' GDP 197 A 1 HETATM 14 O O3' GDP . . . D 3 42.626 19.076 -4.035 1 30.43 ? O3' GDP 197 A 1 HETATM 15 C C2' GDP . . . D 3 41.368 20.584 -5.35 1 33.24 ? C2' GDP 197 A 1 HETATM 16 O O2' GDP . . . D 3 42.579 21.34 -5.265 1 35.55 ? O2' GDP 197 A 1 HETATM 17 C C1' GDP . . . D 3 41.464 19.693 -6.598 1 34.01 ? C1' GDP 197 A 1 HETATM 18 N N9 GDP . . . D 3 41.054 20.442 -7.819 1 32.2 ? N9 GDP 197 A 1 HETATM 19 C C8 GDP . . . D 3 39.947 21.181 -7.948 1 29.05 ? C8 GDP 197 A 1 HETATM 20 N N7 GDP . . . D 3 39.877 21.67 -9.223 1 30.26 ? N7 GDP 197 A 1 HETATM 21 C C5 GDP . . . D 3 40.951 21.251 -9.888 1 27.3 ? C5 GDP 197 A 1 HETATM 22 C C6 GDP . . . D 3 41.47 21.465 -11.248 1 27.52 ? C6 GDP 197 A 1 HETATM 23 O O6 GDP . . . D 3 40.787 22.152 -12.08 1 31.31 ? O6 GDP 197 A 1 HETATM 24 N N1 GDP . . . D 3 42.604 20.825 -11.546 1 26.49 ? N1 GDP 197 A 1 HETATM 25 C C2 GDP . . . D 3 43.277 20.034 -10.702 1 30.35 ? C2 GDP 197 A 1 HETATM 26 N N2 GDP . . . D 3 44.425 19.462 -11.126 1 30.87 ? N2 GDP 197 A 1 HETATM 27 N N3 GDP . . . D 3 42.855 19.822 -9.416 1 30.84 ? N3 GDP 197 A 1 HETATM 28 C C4 GDP . . . D 3 41.72 20.42 -8.977 1 28.16 ? C4 GDP 197 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #