data_7WZC # _model_server_result.job_id Ua-XVnLWpPYT4pemd7Ip1A _model_server_result.datetime_utc '2024-10-11 06:24:26' _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 7wzc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 7WZC # _exptl.entry_id 7WZC _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 7WZC _cell.length_a 31.487 _cell.length_b 66.358 _cell.length_c 83.363 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WZC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 metalc ? metalc1 A OG1 THR 23 A THR 19 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 A O THR 41 A THR 37 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc3 C O1B GDP . A GDP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 D MG MG . A MG 203 1_555 E O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc5 D MG MG . A MG 203 1_555 E O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 D MG MG . A MG 203 1_555 E O HOH . A HOH 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? # _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 7WZC _atom_sites.fract_transf_matrix[1][1] 0.031759 _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] 0.01507 _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] 0.011996 _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 GOL A 1 201 2 GOL GOL . C 3 GDP A 1 202 1 GDP GDP . D 4 MG A 1 203 1 MG MG . E 5 HOH A 1 301 76 HOH HOH . E 5 HOH A 2 302 62 HOH HOH . E 5 HOH A 3 303 67 HOH HOH . E 5 HOH A 4 304 22 HOH HOH . E 5 HOH A 5 305 32 HOH HOH . E 5 HOH A 6 306 85 HOH HOH . E 5 HOH A 7 307 54 HOH HOH . E 5 HOH A 8 308 74 HOH HOH . E 5 HOH A 9 309 105 HOH HOH . E 5 HOH A 10 310 40 HOH HOH . E 5 HOH A 11 311 36 HOH HOH . E 5 HOH A 12 312 55 HOH HOH . E 5 HOH A 13 313 99 HOH HOH . E 5 HOH A 14 314 107 HOH HOH . E 5 HOH A 15 315 53 HOH HOH . E 5 HOH A 16 316 13 HOH HOH . E 5 HOH A 17 317 102 HOH HOH . E 5 HOH A 18 318 14 HOH HOH . E 5 HOH A 19 319 21 HOH HOH . E 5 HOH A 20 320 44 HOH HOH . E 5 HOH A 21 321 1 HOH HOH . E 5 HOH A 22 322 25 HOH HOH . E 5 HOH A 23 323 33 HOH HOH . E 5 HOH A 24 324 51 HOH HOH . E 5 HOH A 25 325 52 HOH HOH . E 5 HOH A 26 326 19 HOH HOH . E 5 HOH A 27 327 31 HOH HOH . E 5 HOH A 28 328 48 HOH HOH . E 5 HOH A 29 329 10 HOH HOH . E 5 HOH A 30 330 24 HOH HOH . E 5 HOH A 31 331 63 HOH HOH . E 5 HOH A 32 332 97 HOH HOH . E 5 HOH A 33 333 77 HOH HOH . E 5 HOH A 34 334 72 HOH HOH . E 5 HOH A 35 335 56 HOH HOH . E 5 HOH A 36 336 58 HOH HOH . E 5 HOH A 37 337 5 HOH HOH . E 5 HOH A 38 338 4 HOH HOH . E 5 HOH A 39 339 6 HOH HOH . E 5 HOH A 40 340 45 HOH HOH . E 5 HOH A 41 341 80 HOH HOH . E 5 HOH A 42 342 3 HOH HOH . E 5 HOH A 43 343 7 HOH HOH . E 5 HOH A 44 344 20 HOH HOH . E 5 HOH A 45 345 43 HOH HOH . E 5 HOH A 46 346 57 HOH HOH . E 5 HOH A 47 347 118 HOH HOH . E 5 HOH A 48 348 11 HOH HOH . E 5 HOH A 49 349 27 HOH HOH . E 5 HOH A 50 350 26 HOH HOH . E 5 HOH A 51 351 94 HOH HOH . E 5 HOH A 52 352 59 HOH HOH . E 5 HOH A 53 353 83 HOH HOH . E 5 HOH A 54 354 34 HOH HOH . E 5 HOH A 55 355 96 HOH HOH . E 5 HOH A 56 356 39 HOH HOH . E 5 HOH A 57 357 17 HOH HOH . E 5 HOH A 58 358 100 HOH HOH . E 5 HOH A 59 359 65 HOH HOH . E 5 HOH A 60 360 88 HOH HOH . E 5 HOH A 61 361 42 HOH HOH . E 5 HOH A 62 362 112 HOH HOH . E 5 HOH A 63 363 15 HOH HOH . E 5 HOH A 64 364 46 HOH HOH . E 5 HOH A 65 365 37 HOH HOH . E 5 HOH A 66 366 47 HOH HOH . E 5 HOH A 67 367 90 HOH HOH . E 5 HOH A 68 368 2 HOH HOH . E 5 HOH A 69 369 61 HOH HOH . E 5 HOH A 70 370 16 HOH HOH . E 5 HOH A 71 371 18 HOH HOH . E 5 HOH A 72 372 41 HOH HOH . E 5 HOH A 73 373 8 HOH HOH . E 5 HOH A 74 374 50 HOH HOH . E 5 HOH A 75 375 71 HOH HOH . E 5 HOH A 76 376 9 HOH HOH . E 5 HOH A 77 377 28 HOH HOH . E 5 HOH A 78 378 79 HOH HOH . E 5 HOH A 79 379 110 HOH HOH . E 5 HOH A 80 380 35 HOH HOH . E 5 HOH A 81 381 70 HOH HOH . E 5 HOH A 82 382 60 HOH HOH . E 5 HOH A 83 383 23 HOH HOH . E 5 HOH A 84 384 66 HOH HOH . E 5 HOH A 85 385 108 HOH HOH . E 5 HOH A 86 386 73 HOH HOH . E 5 HOH A 87 387 84 HOH HOH . E 5 HOH A 88 388 30 HOH HOH . E 5 HOH A 89 389 103 HOH HOH . E 5 HOH A 90 390 49 HOH HOH . E 5 HOH A 91 391 91 HOH HOH . E 5 HOH A 92 392 12 HOH HOH . E 5 HOH A 93 393 68 HOH HOH . E 5 HOH A 94 394 81 HOH HOH . E 5 HOH A 95 395 29 HOH HOH . E 5 HOH A 96 396 69 HOH HOH . E 5 HOH A 97 397 82 HOH HOH . E 5 HOH A 98 398 106 HOH HOH . E 5 HOH A 99 399 86 HOH HOH . E 5 HOH A 100 400 98 HOH HOH . E 5 HOH A 101 401 119 HOH HOH . E 5 HOH A 102 402 104 HOH HOH . E 5 HOH A 103 403 78 HOH HOH . E 5 HOH A 104 404 64 HOH HOH . E 5 HOH A 105 405 95 HOH HOH . E 5 HOH A 106 406 109 HOH HOH . E 5 HOH A 107 407 111 HOH HOH . E 5 HOH A 108 408 114 HOH HOH . E 5 HOH A 109 409 87 HOH HOH . E 5 HOH A 110 410 38 HOH HOH . E 5 HOH A 111 411 101 HOH HOH . E 5 HOH A 112 412 115 HOH HOH . E 5 HOH A 113 413 113 HOH HOH . E 5 HOH A 114 414 92 HOH HOH . E 5 HOH A 115 415 116 HOH HOH . E 5 HOH A 116 416 117 HOH HOH . E 5 HOH A 117 417 75 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 -12.603 2.038 -1.279 1 11.48 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 -12.981 2.06 -2.744 1 11.46 -1 O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 -13.614 1.363 -0.381 1 11.12 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 -11.167 1.722 -0.941 1 12.37 -1 O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 -12.785 3.612 -0.791 1 11.81 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 -13.626 4.651 -1.51 1 12.97 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 -12.975 5.441 -2.617 1 12.9 -1 O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 -15.09 4.371 -1.556 1 13.88 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 -13.611 5.983 -0.312 1 13.95 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 -13.828 5.61 0.957 1 16.28 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 -14.098 6.913 1.789 1 15.25 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 -12.891 7.632 1.961 1 16.27 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 -15.075 7.858 1.055 1 20.57 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 -15.793 8.524 2.056 1 22.71 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 -14.123 8.81 0.312 1 19.16 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 -14.639 10.065 0.077 1 19.62 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 -12.997 8.934 1.398 1 14.61 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 -11.699 9.198 0.809 1 14.11 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 -11.041 8.505 -0.251 1 14.14 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 -9.809 9.003 -0.479 1 14.83 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 -9.651 10.012 0.456 1 14.04 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 -8.517 10.873 0.635 1 12.45 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 -7.444 10.939 0.064 1 15.49 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 -8.712 11.784 1.691 1 19 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 -9.898 11.83 2.444 1 14.84 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 -9.942 12.783 3.452 1 22.16 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 -10.982 11.046 2.307 1 15.65 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 -10.801 10.129 1.276 1 14.63 ? C4 GDP 202 A 1 HETATM 29 H H5' GDP . . . C 3 -13.11 5.106 1.37 1 19.54 ? H5' GDP 202 A 1 HETATM 30 H "H5''" GDP . . . C 3 -14.627 5.078 1.095 1 19.54 ? "H5''" GDP 202 A 1 HETATM 31 H H4' GDP . . . C 3 -14.412 6.666 2.672 1 18.3 ? H4' GDP 202 A 1 HETATM 32 H H3' GDP . . . C 3 -15.643 7.374 0.434 1 24.69 ? H3' GDP 202 A 1 HETATM 33 H HO3' GDP . . . C 3 -16.43 8.015 2.298 1 27.25 ? HO3' GDP 202 A 1 HETATM 34 H H2' GDP . . . C 3 -13.786 8.406 -0.503 1 22.99 ? H2' GDP 202 A 1 HETATM 35 H HO2' GDP . . . C 3 -14.735 10.128 -0.765 1 23.54 ? HO2' GDP 202 A 1 HETATM 36 H H1' GDP . . . C 3 -13.184 9.614 2.065 1 17.54 ? H1' GDP 202 A 1 HETATM 37 H H8 GDP . . . C 3 -11.451 7.809 -0.711 1 16.97 ? H8 GDP 202 A 1 HETATM 38 H HN1 GDP . . . C 3 -8.069 12.331 1.857 1 22.8 ? HN1 GDP 202 A 1 HETATM 39 H HN21 GDP . . . C 3 -9.278 13.312 3.59 1 26.59 ? HN21 GDP 202 A 1 HETATM 40 H HN22 GDP . . . C 3 -10.647 12.846 3.942 1 26.59 ? HN22 GDP 202 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #