data_5VBM # _model_server_result.job_id lIbkCCsVpftcFJLkXiMQRQ _model_server_result.datetime_utc '2024-11-05 06:40:59' _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 5vbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5VBM # _exptl.entry_id 5VBM _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 5VBM _cell.length_a 32.6 _cell.length_b 41.18 _cell.length_c 111.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VBM _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 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 3 _struct_asym.id C _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 73 A CYS 72 1_555 D S24 92V . A 92V 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 B MG MG . A MG 201 1_555 C O3B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc3 B MG MG . A MG 201 1_555 E O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc4 B MG MG . A MG 201 1_555 E O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc5 B MG MG . A MG 201 1_555 E O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc6 B MG MG . A MG 201 1_555 E O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? # _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 124 n n PB O2B GDP sing 125 n n PB O3B GDP sing 126 n n PB O3A GDP sing 127 n n O2B HOB2 GDP sing 128 n n O3B HOB3 GDP sing 129 n n O3A PA GDP sing 130 n n PA O1A GDP doub 131 n n PA O2A GDP sing 132 n n PA O5' GDP sing 133 n n O2A HOA2 GDP sing 134 n n O5' C5' GDP sing 135 n n C5' C4' GDP sing 136 n n C5' H5' GDP sing 137 n n C5' "H5''" GDP sing 138 n n C4' O4' GDP sing 139 n n C4' C3' GDP sing 140 n n C4' H4' GDP sing 141 n n O4' C1' GDP sing 142 n n C3' O3' GDP sing 143 n n C3' C2' GDP sing 144 n n C3' H3' GDP sing 145 n n O3' HO3' GDP sing 146 n n C2' O2' GDP sing 147 n n C2' C1' GDP sing 148 n n C2' H2' GDP sing 149 n n O2' HO2' GDP sing 150 n n C1' N9 GDP sing 151 n n C1' H1' GDP sing 152 n n N9 C8 GDP sing 153 n y N9 C4 GDP sing 154 n y C8 N7 GDP doub 155 n y C8 H8 GDP sing 156 n n N7 C5 GDP sing 157 n y C5 C6 GDP sing 158 n n C5 C4 GDP doub 159 n y C6 O6 GDP doub 160 n n C6 N1 GDP sing 161 n n N1 C2 GDP sing 162 n n N1 HN1 GDP sing 163 n n C2 N2 GDP sing 164 n n C2 N3 GDP doub 165 n n N2 HN21 GDP sing 166 n n N2 HN22 GDP sing 167 n n N3 C4 GDP sing 168 n n # _atom_sites.entry_id 5VBM _atom_sites.fract_transf_matrix[1][1] 0.030675 _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] 0.024284 _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] 0.009001 _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 1 201 200 MG MG . C 3 GDP A 1 202 203 GDP GDP . D 4 92V A 1 203 251 92V LIG . E 5 HOH A 1 301 256 HOH HOH . E 5 HOH A 2 302 79 HOH HOH . E 5 HOH A 3 303 49 HOH HOH . E 5 HOH A 4 304 17 HOH HOH . E 5 HOH A 5 305 53 HOH HOH . E 5 HOH A 6 306 85 HOH HOH . E 5 HOH A 7 307 94 HOH HOH . E 5 HOH A 8 308 65 HOH HOH . E 5 HOH A 9 309 35 HOH HOH . E 5 HOH A 10 310 88 HOH HOH . E 5 HOH A 11 311 23 HOH HOH . E 5 HOH A 12 312 250 HOH HOH . E 5 HOH A 13 313 109 HOH HOH . E 5 HOH A 14 314 50 HOH HOH . E 5 HOH A 15 315 51 HOH HOH . E 5 HOH A 16 316 73 HOH HOH . E 5 HOH A 17 317 1 HOH HOH . E 5 HOH A 18 318 63 HOH HOH . E 5 HOH A 19 319 37 HOH HOH . E 5 HOH A 20 320 8 HOH HOH . E 5 HOH A 21 321 52 HOH HOH . E 5 HOH A 22 322 2 HOH HOH . E 5 HOH A 23 323 6 HOH HOH . E 5 HOH A 24 324 75 HOH HOH . E 5 HOH A 25 325 116 HOH HOH . E 5 HOH A 26 326 48 HOH HOH . E 5 HOH A 27 327 93 HOH HOH . E 5 HOH A 28 328 30 HOH HOH . E 5 HOH A 29 329 128 HOH HOH . E 5 HOH A 30 330 36 HOH HOH . E 5 HOH A 31 331 58 HOH HOH . E 5 HOH A 32 332 74 HOH HOH . E 5 HOH A 33 333 19 HOH HOH . E 5 HOH A 34 334 12 HOH HOH . E 5 HOH A 35 335 78 HOH HOH . E 5 HOH A 36 336 110 HOH HOH . E 5 HOH A 37 337 87 HOH HOH . E 5 HOH A 38 338 99 HOH HOH . E 5 HOH A 39 339 9 HOH HOH . E 5 HOH A 40 340 4 HOH HOH . E 5 HOH A 41 341 26 HOH HOH . E 5 HOH A 42 342 14 HOH HOH . E 5 HOH A 43 343 96 HOH HOH . E 5 HOH A 44 344 13 HOH HOH . E 5 HOH A 45 345 11 HOH HOH . E 5 HOH A 46 346 5 HOH HOH . E 5 HOH A 47 347 90 HOH HOH . E 5 HOH A 48 348 42 HOH HOH . E 5 HOH A 49 349 45 HOH HOH . E 5 HOH A 50 350 29 HOH HOH . E 5 HOH A 51 351 248 HOH HOH . E 5 HOH A 52 352 70 HOH HOH . E 5 HOH A 53 353 118 HOH HOH . E 5 HOH A 54 354 3 HOH HOH . E 5 HOH A 55 355 253 HOH HOH . E 5 HOH A 56 356 72 HOH HOH . E 5 HOH A 57 357 31 HOH HOH . E 5 HOH A 58 358 68 HOH HOH . E 5 HOH A 59 359 15 HOH HOH . E 5 HOH A 60 360 81 HOH HOH . E 5 HOH A 61 361 113 HOH HOH . E 5 HOH A 62 362 124 HOH HOH . E 5 HOH A 63 363 41 HOH HOH . E 5 HOH A 64 364 84 HOH HOH . E 5 HOH A 65 365 62 HOH HOH . E 5 HOH A 66 366 21 HOH HOH . E 5 HOH A 67 367 82 HOH HOH . E 5 HOH A 68 368 32 HOH HOH . E 5 HOH A 69 369 7 HOH HOH . E 5 HOH A 70 370 125 HOH HOH . E 5 HOH A 71 371 77 HOH HOH . E 5 HOH A 72 372 64 HOH HOH . E 5 HOH A 73 373 131 HOH HOH . E 5 HOH A 74 374 16 HOH HOH . E 5 HOH A 75 375 39 HOH HOH . E 5 HOH A 76 376 251 HOH HOH . E 5 HOH A 77 377 24 HOH HOH . E 5 HOH A 78 378 80 HOH HOH . E 5 HOH A 79 379 60 HOH HOH . E 5 HOH A 80 380 55 HOH HOH . E 5 HOH A 81 381 27 HOH HOH . E 5 HOH A 82 382 28 HOH HOH . E 5 HOH A 83 383 243 HOH HOH . E 5 HOH A 84 384 34 HOH HOH . E 5 HOH A 85 385 111 HOH HOH . E 5 HOH A 86 386 83 HOH HOH . E 5 HOH A 87 387 33 HOH HOH . E 5 HOH A 88 388 25 HOH HOH . E 5 HOH A 89 389 71 HOH HOH . E 5 HOH A 90 390 20 HOH HOH . E 5 HOH A 91 391 40 HOH HOH . E 5 HOH A 92 392 38 HOH HOH . E 5 HOH A 93 393 10 HOH HOH . E 5 HOH A 94 394 69 HOH HOH . E 5 HOH A 95 395 115 HOH HOH . E 5 HOH A 96 396 89 HOH HOH . E 5 HOH A 97 397 54 HOH HOH . E 5 HOH A 98 398 92 HOH HOH . E 5 HOH A 99 399 114 HOH HOH . E 5 HOH A 100 400 137 HOH HOH . E 5 HOH A 101 401 107 HOH HOH . E 5 HOH A 102 402 76 HOH HOH . E 5 HOH A 103 403 46 HOH HOH . E 5 HOH A 104 404 252 HOH HOH . E 5 HOH A 105 405 121 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 . . . C 3 -7.155 10.222 17.869 1 10.89 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 -6.948 9.396 16.625 1 11.79 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 -5.962 11.103 18.177 1 13.38 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 -7.577 9.469 19.094 1 10.98 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 -8.355 11.176 17.403 1 10.93 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 -9.544 11.866 18.273 1 12.84 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 -10.652 10.89 18.591 1 14.04 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 -8.969 12.607 19.471 1 12.55 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 -10.147 12.916 17.224 1 12.76 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 -9.268 13.92 16.725 1 12.99 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 -10.097 15.096 16.267 1 10.27 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 -10.971 14.725 15.192 1 12.62 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 -11.014 15.59 17.367 1 11.5 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 -11.096 17.022 17.281 1 17.8 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 -12.348 14.945 17.071 1 13.71 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 -13.496 15.696 17.439 1 16.88 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 -12.346 14.887 15.572 1 11.28 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 -13.015 13.731 14.983 1 13.68 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 -12.783 12.42 15.223 1 10.88 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 -13.557 11.661 14.412 1 11.88 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 -14.268 12.496 13.637 1 13.2 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 -15.255 12.352 12.575 1 13.5 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 -15.606 11.229 12.166 1 12.33 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 -15.717 13.487 12.038 1 11.79 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 -15.338 14.716 12.443 1 14.96 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 -15.876 15.797 11.845 1 15.29 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 -14.443 14.929 13.41 1 14.69 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 -13.897 13.856 14.014 1 11.83 ? C4 GDP 202 A 1 HETATM 29 H H4' GDP . . . C 3 -9.43 15.913 15.956 1 12.32 ? H4' GDP 202 A 1 HETATM 30 H H3' GDP . . . C 3 -10.641 15.264 18.349 1 13.8 ? H3' GDP 202 A 1 HETATM 31 H H2' GDP . . . C 3 -12.38 13.928 17.487 1 16.46 ? H2' GDP 202 A 1 HETATM 32 H HO2' GDP . . . C 3 -13.51 15.814 18.399 1 20.26 ? HO2' GDP 202 A 1 HETATM 33 H H1' GDP . . . C 3 -12.753 15.823 15.165 1 13.54 ? H1' GDP 202 A 1 HETATM 34 H H8 GDP . . . C 3 -12.092 12.036 15.963 1 13.06 ? H8 GDP 202 A 1 HETATM 35 H HN1 GDP . . . C 3 -16.432 13.418 11.286 1 14.14 ? HN1 GDP 202 A 1 HETATM 36 H HN21 GDP . . . C 3 -15.594 16.724 12.128 1 18.35 ? HN21 GDP 202 A 1 HETATM 37 H HN22 GDP . . . C 3 -16.56 15.68 11.111 1 18.35 ? HN22 GDP 202 A 1 # _model_server_stats.io_time_ms 105 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #