data_5V6S # _model_server_result.job_id jQT-BLi7tA_k9SJOZCz0DQ _model_server_result.datetime_utc '2024-10-18 16:28:45' _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 5v6s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5V6S # _exptl.entry_id 5V6S _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 5V6S _cell.length_a 41.07 _cell.length_b 41.07 _cell.length_c 349.446 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V6S _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 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 _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 C27 8YD . A 8YD 203 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.828 ? covale ? covale2 A SG CYS 13 A CYS 12 1_555 D C27 8YD . A 8YD 203 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _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 141 n n PB O2B GDP sing 142 n n PB O3B GDP sing 143 n n PB O3A GDP sing 144 n n O2B HOB2 GDP sing 145 n n O3B HOB3 GDP sing 146 n n O3A PA GDP sing 147 n n PA O1A GDP doub 148 n n PA O2A GDP sing 149 n n PA O5' GDP sing 150 n n O2A HOA2 GDP sing 151 n n O5' C5' GDP sing 152 n n C5' C4' GDP sing 153 n n C5' H5' GDP sing 154 n n C5' "H5''" GDP sing 155 n n C4' O4' GDP sing 156 n n C4' C3' GDP sing 157 n n C4' H4' GDP sing 158 n n O4' C1' GDP sing 159 n n C3' O3' GDP sing 160 n n C3' C2' GDP sing 161 n n C3' H3' GDP sing 162 n n O3' HO3' GDP sing 163 n n C2' O2' GDP sing 164 n n C2' C1' GDP sing 165 n n C2' H2' GDP sing 166 n n O2' HO2' GDP sing 167 n n C1' N9 GDP sing 168 n n C1' H1' GDP sing 169 n n N9 C8 GDP sing 170 n y N9 C4 GDP sing 171 n y C8 N7 GDP doub 172 n y C8 H8 GDP sing 173 n n N7 C5 GDP sing 174 n y C5 C6 GDP sing 175 n n C5 C4 GDP doub 176 n y C6 O6 GDP doub 177 n n C6 N1 GDP sing 178 n n N1 C2 GDP sing 179 n n N1 HN1 GDP sing 180 n n C2 N2 GDP sing 181 n n C2 N3 GDP doub 182 n n N2 HN21 GDP sing 183 n n N2 HN22 GDP sing 184 n n N3 C4 GDP sing 185 n n # _atom_sites.entry_id 5V6S _atom_sites.fract_transf_matrix[1][1] 0.024349 _atom_sites.fract_transf_matrix[1][2] 0.014058 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028115 _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] 0.002862 _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 1 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 8YD A 1 203 1 8YD LIG . E 5 HOH A 1 301 45 HOH HOH . E 5 HOH A 2 302 32 HOH HOH . E 5 HOH A 3 303 56 HOH HOH . E 5 HOH A 4 304 55 HOH HOH . E 5 HOH A 5 305 6 HOH HOH . E 5 HOH A 6 306 8 HOH HOH . E 5 HOH A 7 307 31 HOH HOH . E 5 HOH A 8 308 2 HOH HOH . E 5 HOH A 9 309 5 HOH HOH . E 5 HOH A 10 310 36 HOH HOH . E 5 HOH A 11 311 76 HOH HOH . E 5 HOH A 12 312 19 HOH HOH . E 5 HOH A 13 313 21 HOH HOH . E 5 HOH A 14 314 28 HOH HOH . E 5 HOH A 15 315 37 HOH HOH . E 5 HOH A 16 316 4 HOH HOH . E 5 HOH A 17 317 43 HOH HOH . E 5 HOH A 18 318 65 HOH HOH . E 5 HOH A 19 319 29 HOH HOH . E 5 HOH A 20 320 34 HOH HOH . E 5 HOH A 21 321 7 HOH HOH . E 5 HOH A 22 322 50 HOH HOH . E 5 HOH A 23 323 26 HOH HOH . E 5 HOH A 24 324 9 HOH HOH . E 5 HOH A 25 325 12 HOH HOH . E 5 HOH A 26 326 13 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 3 HOH HOH . E 5 HOH A 29 329 16 HOH HOH . E 5 HOH A 30 330 38 HOH HOH . E 5 HOH A 31 331 22 HOH HOH . E 5 HOH A 32 332 54 HOH HOH . E 5 HOH A 33 333 42 HOH HOH . E 5 HOH A 34 334 61 HOH HOH . E 5 HOH A 35 335 58 HOH HOH . E 5 HOH A 36 336 15 HOH HOH . E 5 HOH A 37 337 48 HOH HOH . E 5 HOH A 38 338 62 HOH HOH . E 5 HOH A 39 339 10 HOH HOH . E 5 HOH A 40 340 78 HOH HOH . E 5 HOH A 41 341 66 HOH HOH . E 5 HOH A 42 342 51 HOH HOH . E 5 HOH A 43 343 25 HOH HOH . E 5 HOH A 44 344 1 HOH HOH . E 5 HOH A 45 345 75 HOH HOH . E 5 HOH A 46 346 53 HOH HOH . E 5 HOH A 47 347 17 HOH HOH . E 5 HOH A 48 348 71 HOH HOH . E 5 HOH A 49 349 70 HOH HOH . E 5 HOH A 50 350 24 HOH HOH . E 5 HOH A 51 351 44 HOH HOH . E 5 HOH A 52 352 49 HOH HOH . E 5 HOH A 53 353 18 HOH HOH . E 5 HOH A 54 354 64 HOH HOH . E 5 HOH A 55 355 47 HOH HOH . E 5 HOH A 56 356 63 HOH HOH . E 5 HOH A 57 357 30 HOH HOH . E 5 HOH A 58 358 33 HOH HOH . E 5 HOH A 59 359 14 HOH HOH . E 5 HOH A 60 360 39 HOH HOH . E 5 HOH A 61 361 46 HOH HOH . E 5 HOH A 62 362 68 HOH HOH . E 5 HOH A 63 363 40 HOH HOH . E 5 HOH A 64 364 41 HOH HOH . E 5 HOH A 65 365 23 HOH HOH . E 5 HOH A 66 366 20 HOH HOH . E 5 HOH A 67 367 60 HOH HOH . E 5 HOH A 68 368 59 HOH HOH . E 5 HOH A 69 369 57 HOH HOH . E 5 HOH A 70 370 52 HOH HOH . E 5 HOH A 71 371 77 HOH HOH . E 5 HOH A 72 372 69 HOH HOH . E 5 HOH A 73 373 72 HOH HOH . E 5 HOH A 74 374 74 HOH HOH . E 5 HOH A 75 375 73 HOH HOH . E 5 HOH A 76 376 35 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 -18.249 14.53 -13.359 1 7.34 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -19.1 15.414 -14.326 1 8.18 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -17.293 13.622 -14.157 1 8.29 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -17.478 15.39 -12.349 1 8.95 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -19.211 13.538 -12.541 1 9.54 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -19.822 13.703 -11.094 1 10.13 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -20.489 15.05 -11.009 1 10.24 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -18.763 13.403 -10.066 1 9.36 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -20.894 12.509 -11.043 1 9.72 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -21.979 12.506 -11.967 1 11.57 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -23.093 11.716 -11.367 1 13.27 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -22.846 10.408 -11.284 1 12.1 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -23.331 12.188 -9.809 1 15.9 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -24.817 12.224 -9.661 1 17.59 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -22.767 11.318 -9.079 1 12.65 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -23.442 11.141 -7.775 1 16.08 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -22.856 9.939 -9.887 1 11.28 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -21.787 9.149 -9.681 1 12.07 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -20.442 9.384 -9.767 1 9.72 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -19.745 8.252 -9.538 1 9.85 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -20.669 7.264 -9.341 1 8.11 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -20.503 5.793 -9.026 1 13 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -19.431 5.251 -8.942 1 12.54 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -21.655 5.031 -8.865 1 13.61 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -22.925 5.615 -8.968 1 15.06 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -24.046 4.811 -8.782 1 16.58 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -23.093 7.02 -9.262 1 11.27 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -21.918 7.833 -9.429 1 12.03 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . B 2 -22.264 13.387 -12.125 1 13.89 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . B 2 -21.692 12.089 -12.816 1 13.89 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . B 2 -23.911 11.861 -11.88 1 15.93 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . B 2 -22.937 13.091 -9.65 1 19.09 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . B 2 -25.167 11.601 -10.138 1 21.11 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . B 2 -21.762 11.578 -8.928 1 15.18 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . B 2 -22.829 11.226 -7.101 1 19.29 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . B 2 -23.711 9.454 -9.678 1 13.53 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . B 2 -20.05 10.235 -9.95 1 11.66 ? H8 GDP 201 A 1 HETATM 38 H HN1 GDP . . . B 2 -21.582 4.14 -8.679 1 16.33 ? HN1 GDP 201 A 1 HETATM 39 H HN21 GDP . . . B 2 -24.862 5.162 -8.855 1 19.89 ? HN21 GDP 201 A 1 HETATM 40 H HN22 GDP . . . B 2 -23.944 3.897 -8.604 1 19.89 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #