data_6ARK # _model_server_result.job_id 43_IEmr8cESM3uevj3_J4w _model_server_result.datetime_utc '2024-11-25 16:06:12' _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 6ark # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6ARK # _exptl.entry_id 6ARK _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 120 _cell.entry_id 6ARK _cell.length_a 94.28 _cell.length_b 94.28 _cell.length_c 119.55 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ARK _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C07 BQD . A BQD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.777 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc3 C MG MG . A MG 202 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 C MG MG . A MG 202 1_555 G O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc5 C MG MG . A MG 202 1_555 G O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 C MG MG . A MG 202 1_555 G O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? # _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 128 n n PB O2B GDP sing 129 n n PB O3B GDP sing 130 n n PB O3A GDP sing 131 n n O2B HOB2 GDP sing 132 n n O3B HOB3 GDP sing 133 n n O3A PA GDP sing 134 n n PA O1A GDP doub 135 n n PA O2A GDP sing 136 n n PA O5' GDP sing 137 n n O2A HOA2 GDP sing 138 n n O5' C5' GDP sing 139 n n C5' C4' GDP sing 140 n n C5' H5' GDP sing 141 n n C5' "H5''" GDP sing 142 n n C4' O4' GDP sing 143 n n C4' C3' GDP sing 144 n n C4' H4' GDP sing 145 n n O4' C1' GDP sing 146 n n C3' O3' GDP sing 147 n n C3' C2' GDP sing 148 n n C3' H3' GDP sing 149 n n O3' HO3' GDP sing 150 n n C2' O2' GDP sing 151 n n C2' C1' GDP sing 152 n n C2' H2' GDP sing 153 n n O2' HO2' GDP sing 154 n n C1' N9 GDP sing 155 n n C1' H1' GDP sing 156 n n N9 C8 GDP sing 157 n y N9 C4 GDP sing 158 n y C8 N7 GDP doub 159 n y C8 H8 GDP sing 160 n n N7 C5 GDP sing 161 n y C5 C6 GDP sing 162 n n C5 C4 GDP doub 163 n y C6 O6 GDP doub 164 n n C6 N1 GDP sing 165 n n N1 C2 GDP sing 166 n n N1 HN1 GDP sing 167 n n C2 N2 GDP sing 168 n n C2 N3 GDP doub 169 n n N2 HN21 GDP sing 170 n n N2 HN22 GDP sing 171 n n N3 C4 GDP sing 172 n n # _atom_sites.entry_id 6ARK _atom_sites.fract_transf_matrix[1][1] 0.010607 _atom_sites.fract_transf_matrix[1][2] 0.006124 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012248 _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] 0.008365 _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 1 201 170 GDP GDP . C 3 MG A 1 202 171 MG MG . D 4 BQD A 1 203 172 BQD LIG . E 5 GOL A 1 204 173 GOL GOL . F 5 GOL A 1 205 174 GOL GOL . G 6 HOH A 1 301 210 HOH HOH . G 6 HOH A 2 302 193 HOH HOH . G 6 HOH A 3 303 228 HOH HOH . G 6 HOH A 4 304 215 HOH HOH . G 6 HOH A 5 305 220 HOH HOH . G 6 HOH A 6 306 214 HOH HOH . G 6 HOH A 7 307 194 HOH HOH . G 6 HOH A 8 308 219 HOH HOH . G 6 HOH A 9 309 189 HOH HOH . G 6 HOH A 10 310 195 HOH HOH . G 6 HOH A 11 311 230 HOH HOH . G 6 HOH A 12 312 201 HOH HOH . G 6 HOH A 13 313 187 HOH HOH . G 6 HOH A 14 314 226 HOH HOH . G 6 HOH A 15 315 192 HOH HOH . G 6 HOH A 16 316 224 HOH HOH . G 6 HOH A 17 317 178 HOH HOH . G 6 HOH A 18 318 204 HOH HOH . G 6 HOH A 19 319 200 HOH HOH . G 6 HOH A 20 320 182 HOH HOH . G 6 HOH A 21 321 216 HOH HOH . G 6 HOH A 22 322 181 HOH HOH . G 6 HOH A 23 323 202 HOH HOH . G 6 HOH A 24 324 176 HOH HOH . G 6 HOH A 25 325 206 HOH HOH . G 6 HOH A 26 326 180 HOH HOH . G 6 HOH A 27 327 213 HOH HOH . G 6 HOH A 28 328 207 HOH HOH . G 6 HOH A 29 329 185 HOH HOH . G 6 HOH A 30 330 205 HOH HOH . G 6 HOH A 31 331 197 HOH HOH . G 6 HOH A 32 332 188 HOH HOH . G 6 HOH A 33 333 186 HOH HOH . G 6 HOH A 34 334 183 HOH HOH . G 6 HOH A 35 335 198 HOH HOH . G 6 HOH A 36 336 179 HOH HOH . G 6 HOH A 37 337 227 HOH HOH . G 6 HOH A 38 338 225 HOH HOH . G 6 HOH A 39 339 177 HOH HOH . G 6 HOH A 40 340 190 HOH HOH . G 6 HOH A 41 341 218 HOH HOH . G 6 HOH A 42 342 196 HOH HOH . G 6 HOH A 43 343 191 HOH HOH . G 6 HOH A 44 344 209 HOH HOH . G 6 HOH A 45 345 175 HOH HOH . G 6 HOH A 46 346 221 HOH HOH . G 6 HOH A 47 347 184 HOH HOH . G 6 HOH A 48 348 208 HOH HOH . G 6 HOH A 49 349 211 HOH HOH . G 6 HOH A 50 350 223 HOH HOH . G 6 HOH A 51 351 203 HOH HOH . G 6 HOH A 52 352 217 HOH HOH . G 6 HOH A 53 353 229 HOH HOH . G 6 HOH A 54 354 212 HOH HOH . G 6 HOH A 55 355 222 HOH HOH . G 6 HOH A 56 356 199 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 -8.34 13.899 -21.208 1 34.85 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -9.106 12.963 -22.239 1 40.13 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -9.221 15.033 -20.692 1 44.84 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -7.747 13.056 -20.101 1 35.57 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -7.153 14.59 -22.052 1 33.01 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -6.659 16.087 -21.846 1 38.71 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -7.611 17.096 -22.316 1 37.93 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -6.36 16.257 -20.369 1 46.26 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.345 16.29 -22.747 1 41.28 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -4.256 15.397 -22.563 1 35.83 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -3.033 15.995 -23.149 1 35.11 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -3.02 15.927 -24.468 1 36.99 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -2.953 17.605 -22.757 1 35.93 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -1.524 17.965 -22.47 1 45.54 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -3.353 18.247 -23.723 1 41.55 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -2.618 19.545 -23.839 1 40.08 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -3.023 17.323 -24.998 1 28.22 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.947 17.431 -25.918 1 29.59 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -5.304 17.296 -25.949 1 29.86 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -5.728 17.492 -27.214 1 27.85 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -4.625 17.746 -27.976 1 28.71 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -4.472 18.038 -29.455 1 27.29 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -5.429 18.08 -30.201 1 27.13 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -3.194 18.261 -29.985 1 30.59 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -2.06 18.217 -29.138 1 28.86 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -0.81 18.445 -29.69 1 31.88 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -2.202 17.935 -27.723 1 28.42 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -3.53 17.711 -27.171 1 26.18 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . B 2 -4.125 15.247 -21.646 1 42.99 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . B 2 -4.455 14.539 -23.014 1 42.99 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . B 2 -2.247 15.536 -22.794 1 42.13 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . B 2 -3.523 17.793 -21.96 1 43.11 ? H3' GDP 201 A 1 HETATM 33 H H2' GDP . . . B 2 -4.386 18.414 -23.649 1 49.86 ? H2' GDP 201 A 1 HETATM 34 H HO2' GDP . . . B 2 -2.979 20.039 -24.52 1 48.09 ? HO2' GDP 201 A 1 HETATM 35 H H1' GDP . . . B 2 -2.121 17.556 -25.376 1 33.86 ? H1' GDP 201 A 1 HETATM 36 H H8 GDP . . . B 2 -5.862 17.098 -25.199 1 35.83 ? H8 GDP 201 A 1 HETATM 37 H HN1 GDP . . . B 2 -3.094 18.442 -30.874 1 36.71 ? HN1 GDP 201 A 1 HETATM 38 H HN21 GDP . . . B 2 -0.084 18.417 -29.174 1 38.26 ? HN21 GDP 201 A 1 HETATM 39 H HN22 GDP . . . B 2 -0.726 18.624 -30.606 1 38.26 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #