data_3OKC # _model_server_result.job_id 2Fti5msemJOGxRGnZp_8dw _model_server_result.datetime_utc '2024-11-22 09:05:06' _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 3okc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 3OKC # _exptl.entry_id 3OKC _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 3OKC _cell.length_a 44.852 _cell.length_b 86.4 _cell.length_c 106.639 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OKC _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 _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 # _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 3OKC _atom_sites.fract_transf_matrix[1][1] 0.022296 _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] 0.011574 _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] 0.009377 _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 1 601 601 GDP GDP . C 3 HOH A 1 395 14 HOH HOH . C 3 HOH A 2 396 15 HOH HOH . C 3 HOH A 3 397 16 HOH HOH . C 3 HOH A 4 398 17 HOH HOH . C 3 HOH A 5 399 18 HOH HOH . C 3 HOH A 6 400 19 HOH HOH . C 3 HOH A 7 401 20 HOH HOH . C 3 HOH A 8 402 21 HOH HOH . C 3 HOH A 9 403 22 HOH HOH . C 3 HOH A 10 404 23 HOH HOH . C 3 HOH A 11 405 24 HOH HOH . C 3 HOH A 12 406 25 HOH HOH . C 3 HOH A 13 407 26 HOH HOH . C 3 HOH A 14 408 27 HOH HOH . C 3 HOH A 15 409 28 HOH HOH . C 3 HOH A 16 410 29 HOH HOH . C 3 HOH A 17 411 30 HOH HOH . C 3 HOH A 18 412 31 HOH HOH . C 3 HOH A 19 413 32 HOH HOH . C 3 HOH A 20 414 33 HOH HOH . C 3 HOH A 21 415 34 HOH HOH . C 3 HOH A 22 416 35 HOH HOH . C 3 HOH A 23 417 36 HOH HOH . C 3 HOH A 24 418 37 HOH HOH . C 3 HOH A 25 419 38 HOH HOH . C 3 HOH A 26 420 39 HOH HOH . C 3 HOH A 27 421 40 HOH HOH . C 3 HOH A 28 422 41 HOH HOH . C 3 HOH A 29 423 42 HOH HOH . C 3 HOH A 30 424 43 HOH HOH . C 3 HOH A 31 425 44 HOH HOH . C 3 HOH A 32 426 45 HOH HOH . C 3 HOH A 33 427 46 HOH HOH . C 3 HOH A 34 428 47 HOH HOH . C 3 HOH A 35 429 48 HOH HOH . C 3 HOH A 36 430 49 HOH HOH . C 3 HOH A 37 431 50 HOH HOH . C 3 HOH A 38 432 51 HOH HOH . C 3 HOH A 39 433 52 HOH HOH . C 3 HOH A 40 434 53 HOH HOH . C 3 HOH A 41 435 54 HOH HOH . C 3 HOH A 42 436 55 HOH HOH . C 3 HOH A 43 437 56 HOH HOH . C 3 HOH A 44 438 57 HOH HOH . C 3 HOH A 45 439 58 HOH HOH . C 3 HOH A 46 440 59 HOH HOH . C 3 HOH A 47 441 60 HOH HOH . C 3 HOH A 48 442 61 HOH HOH . C 3 HOH A 49 443 62 HOH HOH . C 3 HOH A 50 444 63 HOH HOH . C 3 HOH A 51 445 64 HOH HOH . C 3 HOH A 52 446 65 HOH HOH . C 3 HOH A 53 447 66 HOH HOH . C 3 HOH A 54 448 67 HOH HOH . C 3 HOH A 55 449 68 HOH HOH . C 3 HOH A 56 450 69 HOH HOH . C 3 HOH A 57 451 70 HOH HOH . C 3 HOH A 58 452 71 HOH HOH . C 3 HOH A 59 453 72 HOH HOH . C 3 HOH A 60 454 73 HOH HOH . C 3 HOH A 61 455 74 HOH HOH . C 3 HOH A 62 456 75 HOH HOH . C 3 HOH A 63 457 76 HOH HOH . C 3 HOH A 64 458 77 HOH HOH . C 3 HOH A 65 459 78 HOH HOH . C 3 HOH A 66 460 79 HOH HOH . C 3 HOH A 67 461 80 HOH HOH . C 3 HOH A 68 462 81 HOH HOH . C 3 HOH A 69 463 82 HOH HOH . C 3 HOH A 70 464 83 HOH HOH . C 3 HOH A 71 465 84 HOH HOH . C 3 HOH A 72 466 85 HOH HOH . C 3 HOH A 73 467 86 HOH HOH . C 3 HOH A 74 468 87 HOH HOH . C 3 HOH A 75 469 88 HOH HOH . C 3 HOH A 76 470 89 HOH HOH . C 3 HOH A 77 471 90 HOH HOH . C 3 HOH A 78 472 91 HOH HOH . C 3 HOH A 79 473 92 HOH HOH . C 3 HOH A 80 474 93 HOH HOH . C 3 HOH A 81 475 94 HOH HOH . C 3 HOH A 82 476 95 HOH HOH . C 3 HOH A 83 477 96 HOH HOH . C 3 HOH A 84 478 97 HOH HOH . C 3 HOH A 85 479 98 HOH HOH . C 3 HOH A 86 480 99 HOH HOH . C 3 HOH A 87 481 100 HOH HOH . C 3 HOH A 88 482 101 HOH HOH . C 3 HOH A 89 483 102 HOH HOH . C 3 HOH A 90 484 103 HOH HOH . C 3 HOH A 91 485 104 HOH HOH . C 3 HOH A 92 486 105 HOH HOH . C 3 HOH A 93 487 106 HOH HOH . C 3 HOH A 94 488 107 HOH HOH . C 3 HOH A 95 489 108 HOH HOH . C 3 HOH A 96 490 109 HOH HOH . C 3 HOH A 97 491 110 HOH HOH . C 3 HOH A 98 492 111 HOH HOH . C 3 HOH A 99 493 112 HOH HOH . C 3 HOH A 100 494 113 HOH HOH . C 3 HOH A 101 495 114 HOH HOH . C 3 HOH A 102 496 115 HOH HOH . C 3 HOH A 103 497 116 HOH HOH . C 3 HOH A 104 498 117 HOH HOH . C 3 HOH A 105 499 118 HOH HOH . C 3 HOH A 106 500 119 HOH HOH . C 3 HOH A 107 501 120 HOH HOH . C 3 HOH A 108 502 121 HOH HOH . C 3 HOH A 109 503 122 HOH HOH . C 3 HOH A 110 504 123 HOH HOH . C 3 HOH A 111 505 124 HOH HOH . C 3 HOH A 112 506 125 HOH HOH . C 3 HOH A 113 507 126 HOH HOH . C 3 HOH A 114 508 127 HOH HOH . C 3 HOH A 115 509 128 HOH HOH . C 3 HOH A 116 510 129 HOH HOH . C 3 HOH A 117 511 130 HOH HOH . C 3 HOH A 118 512 131 HOH HOH . C 3 HOH A 119 513 132 HOH HOH . C 3 HOH A 120 514 133 HOH HOH . C 3 HOH A 121 515 134 HOH HOH . C 3 HOH A 122 516 135 HOH HOH . C 3 HOH A 123 517 136 HOH HOH . C 3 HOH A 124 518 137 HOH HOH . C 3 HOH A 125 519 138 HOH HOH . C 3 HOH A 126 520 139 HOH HOH . C 3 HOH A 127 521 140 HOH HOH . C 3 HOH A 128 522 1 HOH HOH . C 3 HOH A 129 523 2 HOH HOH . C 3 HOH A 130 524 3 HOH HOH . C 3 HOH A 131 525 4 HOH HOH . C 3 HOH A 132 526 5 HOH HOH . C 3 HOH A 133 527 6 HOH HOH . C 3 HOH A 134 528 7 HOH HOH . C 3 HOH A 135 529 8 HOH HOH . C 3 HOH A 136 530 9 HOH HOH . C 3 HOH A 137 531 10 HOH HOH . C 3 HOH A 138 532 11 HOH HOH . C 3 HOH A 139 533 12 HOH HOH . C 3 HOH A 140 534 13 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 4.472 6.08 26.316 1 36.4 ? PB GDP 601 A 1 HETATM 2 O O1B GDP . . . B 2 5.213 5.303 25.33 1 36.41 ? O1B GDP 601 A 1 HETATM 3 O O2B GDP . . . B 2 4.965 5.914 27.449 1 36.75 ? O2B GDP 601 A 1 HETATM 4 O O3B GDP . . . B 2 3.296 5.658 26.34 1 36.15 ? O3B GDP 601 A 1 HETATM 5 O O3A GDP . . . B 2 4.468 7.49 25.954 1 37.36 ? O3A GDP 601 A 1 HETATM 6 P PA GDP . . . B 2 5.587 8.425 26.047 1 37.19 ? PA GDP 601 A 1 HETATM 7 O O1A GDP . . . B 2 5.879 8.636 27.246 1 36.61 ? O1A GDP 601 A 1 HETATM 8 O O2A GDP . . . B 2 5.238 9.519 25.531 1 36.2 ? O2A GDP 601 A 1 HETATM 9 O O5' GDP . . . B 2 6.764 7.916 25.36 1 37.58 ? O5' GDP 601 A 1 HETATM 10 C C5' GDP . . . B 2 6.795 7.77 23.938 1 38.39 ? C5' GDP 601 A 1 HETATM 11 C C4' GDP . . . B 2 8.228 7.824 23.418 1 38.86 ? C4' GDP 601 A 1 HETATM 12 O O4' GDP . . . B 2 8.333 7.094 22.182 1 39.01 ? O4' GDP 601 A 1 HETATM 13 C C3' GDP . . . B 2 8.641 9.264 23.139 1 38.84 ? C3' GDP 601 A 1 HETATM 14 O O3' GDP . . . B 2 9.951 9.508 23.661 1 37.5 ? O3' GDP 601 A 1 HETATM 15 C C2' GDP . . . B 2 8.656 9.375 21.628 1 39.1 ? C2' GDP 601 A 1 HETATM 16 O O2' GDP . . . B 2 9.691 10.256 21.184 1 39.57 ? O2' GDP 601 A 1 HETATM 17 C C1' GDP . . . B 2 8.876 7.94 21.158 1 39.04 ? C1' GDP 601 A 1 HETATM 18 N N9 GDP . . . B 2 8.258 7.721 19.82 1 39.09 ? N9 GDP 601 A 1 HETATM 19 C C8 GDP . . . B 2 6.947 7.661 19.52 1 39 ? C8 GDP 601 A 1 HETATM 20 N N7 GDP . . . B 2 6.806 7.455 18.187 1 38.8 ? N7 GDP 601 A 1 HETATM 21 C C5 GDP . . . B 2 8.046 7.388 17.651 1 38.81 ? C5 GDP 601 A 1 HETATM 22 C C6 GDP . . . B 2 8.53 7.196 16.358 1 38.84 ? C6 GDP 601 A 1 HETATM 23 O O6 GDP . . . B 2 7.739 7.043 15.402 1 38.93 ? O6 GDP 601 A 1 HETATM 24 N N1 GDP . . . B 2 9.867 7.177 16.139 1 38.83 ? N1 GDP 601 A 1 HETATM 25 C C2 GDP . . . B 2 10.74 7.341 17.165 1 38.87 ? C2 GDP 601 A 1 HETATM 26 N N2 GDP . . . B 2 12.074 7.321 16.932 1 38.75 ? N2 GDP 601 A 1 HETATM 27 N N3 GDP . . . B 2 10.29 7.531 18.428 1 38.84 ? N3 GDP 601 A 1 HETATM 28 C C4 GDP . . . B 2 8.955 7.558 18.688 1 39.03 ? C4 GDP 601 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #