data_3P32 # _model_server_result.job_id AaozHJEXnp2JWcQDlEAkiA _model_server_result.datetime_utc '2024-11-07 01:35:17' _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 3p32 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":335}' # _entry.id 3P32 # _exptl.entry_id 3P32 _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 90 _cell.entry_id 3P32 _cell.length_a 65.86 _cell.length_b 188.22 _cell.length_c 66.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P32 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -33.25 # _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 # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3P32 _atom_sites.fract_transf_matrix[1][1] 0.015184 _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] 0.005313 _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] 0.015038 _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 1 335 335 GDP GDP . C 3 PGE A 1 336 336 PGE PGE . D 3 PGE A 1 337 337 PGE PGE . E 4 HOH A 1 338 1 HOH HOH . E 4 HOH A 2 339 2 HOH HOH . E 4 HOH A 3 340 3 HOH HOH . E 4 HOH A 4 341 4 HOH HOH . E 4 HOH A 5 342 5 HOH HOH . E 4 HOH A 6 343 6 HOH HOH . E 4 HOH A 7 344 7 HOH HOH . E 4 HOH A 8 345 8 HOH HOH . E 4 HOH A 9 346 9 HOH HOH . E 4 HOH A 10 347 10 HOH HOH . E 4 HOH A 11 348 11 HOH HOH . E 4 HOH A 12 349 12 HOH HOH . E 4 HOH A 13 350 13 HOH HOH . E 4 HOH A 14 351 14 HOH HOH . E 4 HOH A 15 352 15 HOH HOH . E 4 HOH A 16 353 16 HOH HOH . E 4 HOH A 17 354 17 HOH HOH . E 4 HOH A 18 355 18 HOH HOH . E 4 HOH A 19 356 19 HOH HOH . E 4 HOH A 20 357 20 HOH HOH . E 4 HOH A 21 358 21 HOH HOH . E 4 HOH A 22 359 22 HOH HOH . E 4 HOH A 23 360 23 HOH HOH . E 4 HOH A 24 361 24 HOH HOH . E 4 HOH A 25 362 25 HOH HOH . E 4 HOH A 26 363 26 HOH HOH . E 4 HOH A 27 364 27 HOH HOH . E 4 HOH A 28 365 28 HOH HOH . E 4 HOH A 29 366 29 HOH HOH . E 4 HOH A 30 367 30 HOH HOH . E 4 HOH A 31 368 31 HOH HOH . E 4 HOH A 32 369 32 HOH HOH . E 4 HOH A 33 370 33 HOH HOH . E 4 HOH A 34 371 34 HOH HOH . E 4 HOH A 35 372 35 HOH HOH . E 4 HOH A 36 373 36 HOH HOH . E 4 HOH A 37 374 37 HOH HOH . E 4 HOH A 38 375 38 HOH HOH . E 4 HOH A 39 376 39 HOH HOH . E 4 HOH A 40 377 40 HOH HOH . E 4 HOH A 41 378 41 HOH HOH . E 4 HOH A 42 379 42 HOH HOH . E 4 HOH A 43 380 43 HOH HOH . E 4 HOH A 44 381 44 HOH HOH . E 4 HOH A 45 382 45 HOH HOH . E 4 HOH A 46 383 46 HOH HOH . E 4 HOH A 47 384 47 HOH HOH . E 4 HOH A 48 385 48 HOH HOH . E 4 HOH A 49 386 49 HOH HOH . E 4 HOH A 50 387 50 HOH HOH . E 4 HOH A 51 388 51 HOH HOH . E 4 HOH A 52 389 52 HOH HOH . E 4 HOH A 53 390 53 HOH HOH . E 4 HOH A 54 391 54 HOH HOH . E 4 HOH A 55 392 55 HOH HOH . E 4 HOH A 56 393 56 HOH HOH . E 4 HOH A 57 394 57 HOH HOH . E 4 HOH A 58 395 58 HOH HOH . E 4 HOH A 59 396 59 HOH HOH . E 4 HOH A 60 397 60 HOH HOH . E 4 HOH A 61 398 61 HOH HOH . E 4 HOH A 62 399 62 HOH HOH . E 4 HOH A 63 400 63 HOH HOH . E 4 HOH A 64 401 64 HOH HOH . E 4 HOH A 65 402 65 HOH HOH . E 4 HOH A 66 403 66 HOH HOH . E 4 HOH A 67 404 67 HOH HOH . E 4 HOH A 68 405 68 HOH HOH . E 4 HOH A 69 406 69 HOH HOH . E 4 HOH A 70 407 70 HOH HOH . E 4 HOH A 71 408 71 HOH HOH . E 4 HOH A 72 409 72 HOH HOH . E 4 HOH A 73 410 73 HOH HOH . E 4 HOH A 74 411 74 HOH HOH . E 4 HOH A 75 412 75 HOH HOH . E 4 HOH A 76 413 76 HOH HOH . E 4 HOH A 77 414 77 HOH HOH . E 4 HOH A 78 415 78 HOH HOH . E 4 HOH A 79 416 79 HOH HOH . E 4 HOH A 80 417 80 HOH HOH . E 4 HOH A 81 418 81 HOH HOH . E 4 HOH A 82 419 82 HOH HOH . E 4 HOH A 83 420 83 HOH HOH . E 4 HOH A 84 421 84 HOH HOH . E 4 HOH A 85 422 85 HOH HOH . E 4 HOH A 86 423 86 HOH HOH . E 4 HOH A 87 424 87 HOH HOH . E 4 HOH A 88 425 88 HOH HOH . E 4 HOH A 89 426 89 HOH HOH . E 4 HOH A 90 427 90 HOH HOH . E 4 HOH A 91 428 91 HOH HOH . E 4 HOH A 92 429 92 HOH HOH . E 4 HOH A 93 430 93 HOH HOH . E 4 HOH A 94 431 94 HOH HOH . E 4 HOH A 95 432 95 HOH HOH . E 4 HOH A 96 433 96 HOH HOH . E 4 HOH A 97 434 97 HOH HOH . E 4 HOH A 98 435 98 HOH HOH . E 4 HOH A 99 436 99 HOH HOH . E 4 HOH A 100 437 100 HOH HOH . E 4 HOH A 101 438 101 HOH HOH . E 4 HOH A 102 439 102 HOH HOH . E 4 HOH A 103 440 103 HOH HOH . E 4 HOH A 104 441 104 HOH HOH . E 4 HOH A 105 442 105 HOH HOH . E 4 HOH A 106 443 106 HOH HOH . E 4 HOH A 107 444 107 HOH HOH . E 4 HOH A 108 445 108 HOH HOH . E 4 HOH A 109 446 109 HOH HOH . E 4 HOH A 110 447 110 HOH HOH . E 4 HOH A 111 448 111 HOH HOH . E 4 HOH A 112 449 112 HOH HOH . E 4 HOH A 113 450 113 HOH HOH . E 4 HOH A 114 451 114 HOH HOH . E 4 HOH A 115 452 115 HOH HOH . E 4 HOH A 116 453 116 HOH HOH . E 4 HOH A 117 454 117 HOH HOH . E 4 HOH A 118 455 118 HOH HOH . E 4 HOH A 119 456 119 HOH HOH . E 4 HOH A 120 457 120 HOH HOH . E 4 HOH A 121 458 121 HOH HOH . E 4 HOH A 122 459 122 HOH HOH . E 4 HOH A 123 460 123 HOH HOH . E 4 HOH A 124 461 124 HOH HOH . E 4 HOH A 125 462 125 HOH HOH . E 4 HOH A 126 463 126 HOH HOH . E 4 HOH A 127 464 127 HOH HOH . E 4 HOH A 128 465 128 HOH HOH . E 4 HOH A 129 466 129 HOH HOH . E 4 HOH A 130 467 130 HOH HOH . E 4 HOH A 131 468 131 HOH HOH . E 4 HOH A 132 469 132 HOH HOH . E 4 HOH A 133 470 133 HOH HOH . E 4 HOH A 134 471 134 HOH HOH . E 4 HOH A 135 472 135 HOH HOH . E 4 HOH A 136 473 136 HOH HOH . E 4 HOH A 137 474 137 HOH HOH . E 4 HOH A 138 475 138 HOH HOH . E 4 HOH A 139 476 139 HOH HOH . E 4 HOH A 140 477 140 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 22.896 37.554 -15.185 1 34.75 ? PB GDP 335 A 1 HETATM 2 O O1B GDP . . . B 2 23.351 36.573 -14.136 1 34.21 ? O1B GDP 335 A 1 HETATM 3 O O2B GDP . . . B 2 23.007 36.908 -16.541 1 36.14 ? O2B GDP 335 A 1 HETATM 4 O O3B GDP . . . B 2 21.404 37.838 -15.001 1 35.95 ? O3B GDP 335 A 1 HETATM 5 O O3A GDP . . . B 2 23.613 38.975 -15.179 1 35.75 ? O3A GDP 335 A 1 HETATM 6 P PA GDP . . . B 2 25.07 39.321 -14.55 1 41 ? PA GDP 335 A 1 HETATM 7 O O1A GDP . . . B 2 26.073 38.297 -15.016 1 41.98 ? O1A GDP 335 A 1 HETATM 8 O O2A GDP . . . B 2 25.002 39.492 -13.056 1 38.82 ? O2A GDP 335 A 1 HETATM 9 O O5' GDP . . . B 2 25.286 40.727 -15.244 1 42.38 ? O5' GDP 335 A 1 HETATM 10 C C5' GDP . . . B 2 25.416 40.78 -16.668 1 45.42 ? C5' GDP 335 A 1 HETATM 11 C C4' GDP . . . B 2 26.118 42.082 -17.006 1 46.31 ? C4' GDP 335 A 1 HETATM 12 O O4' GDP . . . B 2 25.329 43.155 -16.474 1 48.16 ? O4' GDP 335 A 1 HETATM 13 C C3' GDP . . . B 2 27.496 42.203 -16.36 1 47.79 ? C3' GDP 335 A 1 HETATM 14 O O3' GDP . . . B 2 28.315 43.027 -17.195 1 46.76 ? O3' GDP 335 A 1 HETATM 15 C C2' GDP . . . B 2 27.231 42.978 -15.086 1 47.78 ? C2' GDP 335 A 1 HETATM 16 O O2' GDP . . . B 2 28.38 43.709 -14.636 1 49.03 ? O2' GDP 335 A 1 HETATM 17 C C1' GDP . . . B 2 26.097 43.897 -15.523 1 47.25 ? C1' GDP 335 A 1 HETATM 18 N N9 GDP . . . B 2 25.291 44.346 -14.355 1 48.11 ? N9 GDP 335 A 1 HETATM 19 C C8 GDP . . . B 2 24.829 43.591 -13.328 1 47.28 ? C8 GDP 335 A 1 HETATM 20 N N7 GDP . . . B 2 24.141 44.36 -12.442 1 47.85 ? N7 GDP 335 A 1 HETATM 21 C C5 GDP . . . B 2 24.159 45.629 -12.906 1 46.25 ? C5 GDP 335 A 1 HETATM 22 C C6 GDP . . . B 2 23.645 46.943 -12.469 1 44.76 ? C6 GDP 335 A 1 HETATM 23 O O6 GDP . . . B 2 22.983 47.065 -11.406 1 42.67 ? O6 GDP 335 A 1 HETATM 24 N N1 GDP . . . B 2 23.904 48.007 -13.258 1 44.78 ? N1 GDP 335 A 1 HETATM 25 C C2 GDP . . . B 2 24.61 47.935 -14.412 1 46.36 ? C2 GDP 335 A 1 HETATM 26 N N2 GDP . . . B 2 24.804 49.064 -15.142 1 45.06 ? N2 GDP 335 A 1 HETATM 27 N N3 GDP . . . B 2 25.111 46.765 -14.869 1 46.04 ? N3 GDP 335 A 1 HETATM 28 C C4 GDP . . . B 2 24.918 45.611 -14.172 1 46.69 ? C4 GDP 335 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #