data_8WOV # _model_server_result.job_id s1BhqIk7ZBXIuIdg2hNd1Q _model_server_result.datetime_utc '2024-11-22 18:45:01' _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 8wov # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 8WOV # _exptl.entry_id 8WOV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 8WOV _cell.length_a 101.49 _cell.length_b 109.243 _cell.length_c 130.627 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WOV _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,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-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 N1 C2 UDP sing 433 n n N1 C6 UDP sing 434 n n N1 C1' UDP sing 435 n n C2 N3 UDP sing 436 n n C2 O2 UDP doub 437 n n N3 C4 UDP sing 438 n n N3 HN3 UDP sing 439 n n C4 C5 UDP sing 440 n n C4 O4 UDP doub 441 n n C5 C6 UDP doub 442 n n C5 H5 UDP sing 443 n n C6 H6 UDP sing 444 n n C1' C2' UDP sing 445 n n C1' O4' UDP sing 446 n n C1' H1' UDP sing 447 n n C2' O2' UDP sing 448 n n C2' C3' UDP sing 449 n n C2' H2' UDP sing 450 n n O2' HO2' UDP sing 451 n n C3' C4' UDP sing 452 n n C3' O3' UDP sing 453 n n C3' H3' UDP sing 454 n n C4' O4' UDP sing 455 n n C4' C5' UDP sing 456 n n C4' H4' UDP sing 457 n n O3' HO3' UDP sing 458 n n C5' O5' UDP sing 459 n n C5' "H5'1" UDP sing 460 n n C5' "H5'2" UDP sing 461 n n O5' PA UDP sing 462 n n PA O1A UDP doub 463 n n PA O2A UDP sing 464 n n PA O3A UDP sing 465 n n O2A HOA2 UDP sing 466 n n O3A PB UDP sing 467 n n PB O1B UDP doub 468 n n PB O2B UDP sing 469 n n PB O3B UDP sing 470 n n O2B HOB2 UDP sing 471 n n O3B HOB3 UDP sing 472 n n # _atom_sites.entry_id 8WOV _atom_sites.fract_transf_matrix[1][1] 0.009853 _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] 0.009154 _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] 0.007655 _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 C 2 NAD B 1 401 401 NAD NAD . D 3 UDP B 1 402 402 UDP UDP . E 3 UDP A 1 401 401 UDP UDP . F 2 NAD A 1 402 402 NAD NAD . G 4 HOH B 1 501 66 HOH HOH . G 4 HOH B 2 502 53 HOH HOH . G 4 HOH B 3 503 18 HOH HOH . G 4 HOH B 4 504 95 HOH HOH . G 4 HOH B 5 505 59 HOH HOH . G 4 HOH B 6 506 11 HOH HOH . G 4 HOH B 7 507 34 HOH HOH . G 4 HOH B 8 508 42 HOH HOH . G 4 HOH B 9 509 81 HOH HOH . G 4 HOH B 10 510 102 HOH HOH . G 4 HOH B 11 511 64 HOH HOH . G 4 HOH B 12 512 8 HOH HOH . G 4 HOH B 13 513 91 HOH HOH . G 4 HOH B 14 514 65 HOH HOH . G 4 HOH B 15 515 84 HOH HOH . G 4 HOH B 16 516 27 HOH HOH . G 4 HOH B 17 517 12 HOH HOH . G 4 HOH B 18 518 51 HOH HOH . G 4 HOH B 19 519 80 HOH HOH . G 4 HOH B 20 520 15 HOH HOH . G 4 HOH B 21 521 69 HOH HOH . G 4 HOH B 22 522 75 HOH HOH . G 4 HOH B 23 523 90 HOH HOH . G 4 HOH B 24 524 56 HOH HOH . G 4 HOH B 25 525 77 HOH HOH . G 4 HOH B 26 526 57 HOH HOH . G 4 HOH B 27 527 79 HOH HOH . G 4 HOH B 28 528 33 HOH HOH . G 4 HOH B 29 529 97 HOH HOH . G 4 HOH B 30 530 20 HOH HOH . G 4 HOH B 31 531 13 HOH HOH . G 4 HOH B 32 532 37 HOH HOH . G 4 HOH B 33 533 21 HOH HOH . G 4 HOH B 34 534 23 HOH HOH . G 4 HOH B 35 535 29 HOH HOH . G 4 HOH B 36 536 48 HOH HOH . G 4 HOH B 37 537 9 HOH HOH . G 4 HOH B 38 538 104 HOH HOH . G 4 HOH B 39 539 105 HOH HOH . G 4 HOH B 40 540 107 HOH HOH . G 4 HOH B 41 541 30 HOH HOH . G 4 HOH B 42 542 47 HOH HOH . G 4 HOH B 43 543 85 HOH HOH . G 4 HOH B 44 544 70 HOH HOH . G 4 HOH B 45 545 44 HOH HOH . G 4 HOH B 46 546 4 HOH HOH . G 4 HOH B 47 547 46 HOH HOH . G 4 HOH B 48 548 88 HOH HOH . H 4 HOH A 1 501 2 HOH HOH . H 4 HOH A 2 502 62 HOH HOH . H 4 HOH A 3 503 38 HOH HOH . H 4 HOH A 4 504 98 HOH HOH . H 4 HOH A 5 505 49 HOH HOH . H 4 HOH A 6 506 31 HOH HOH . H 4 HOH A 7 507 39 HOH HOH . H 4 HOH A 8 508 72 HOH HOH . H 4 HOH A 9 509 43 HOH HOH . H 4 HOH A 10 510 61 HOH HOH . H 4 HOH A 11 511 55 HOH HOH . H 4 HOH A 12 512 14 HOH HOH . H 4 HOH A 13 513 100 HOH HOH . H 4 HOH A 14 514 58 HOH HOH . H 4 HOH A 15 515 78 HOH HOH . H 4 HOH A 16 516 32 HOH HOH . H 4 HOH A 17 517 25 HOH HOH . H 4 HOH A 18 518 35 HOH HOH . H 4 HOH A 19 519 103 HOH HOH . H 4 HOH A 20 520 52 HOH HOH . H 4 HOH A 21 521 74 HOH HOH . H 4 HOH A 22 522 89 HOH HOH . H 4 HOH A 23 523 50 HOH HOH . H 4 HOH A 24 524 5 HOH HOH . H 4 HOH A 25 525 82 HOH HOH . H 4 HOH A 26 526 71 HOH HOH . H 4 HOH A 27 527 6 HOH HOH . H 4 HOH A 28 528 22 HOH HOH . H 4 HOH A 29 529 67 HOH HOH . H 4 HOH A 30 530 93 HOH HOH . H 4 HOH A 31 531 16 HOH HOH . H 4 HOH A 32 532 24 HOH HOH . H 4 HOH A 33 533 40 HOH HOH . H 4 HOH A 34 534 10 HOH HOH . H 4 HOH A 35 535 63 HOH HOH . H 4 HOH A 36 536 28 HOH HOH . H 4 HOH A 37 537 108 HOH HOH . H 4 HOH A 38 538 41 HOH HOH . H 4 HOH A 39 539 99 HOH HOH . H 4 HOH A 40 540 109 HOH HOH . H 4 HOH A 41 541 76 HOH HOH . H 4 HOH A 42 542 86 HOH HOH . H 4 HOH A 43 543 60 HOH HOH . H 4 HOH A 44 544 87 HOH HOH . H 4 HOH A 45 545 101 HOH HOH . H 4 HOH A 46 546 3 HOH HOH . H 4 HOH A 47 547 19 HOH HOH . H 4 HOH A 48 548 1 HOH HOH . H 4 HOH A 49 549 83 HOH HOH . H 4 HOH A 50 550 17 HOH HOH . H 4 HOH A 51 551 45 HOH HOH . H 4 HOH A 52 552 7 HOH HOH . H 4 HOH A 53 553 54 HOH HOH . H 4 HOH A 54 554 96 HOH HOH . H 4 HOH A 55 555 73 HOH HOH . H 4 HOH A 56 556 92 HOH HOH . H 4 HOH A 57 557 36 HOH HOH . H 4 HOH A 58 558 26 HOH HOH . H 4 HOH A 59 559 106 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 N N1 UDP . . . D 3 18.126 -14.623 23.279 1 34.63 ? N1 UDP 402 B 1 HETATM 2 C C2 UDP . . . D 3 17.23 -15.428 22.605 1 32.4 ? C2 UDP 402 B 1 HETATM 3 N N3 UDP . . . D 3 15.922 -14.994 22.663 1 32.78 ? N3 UDP 402 B 1 HETATM 4 C C4 UDP . . . D 3 15.437 -13.853 23.289 1 37.93 ? C4 UDP 402 B 1 HETATM 5 C C5 UDP . . . D 3 16.439 -13.076 23.972 1 37.96 ? C5 UDP 402 B 1 HETATM 6 C C6 UDP . . . D 3 17.719 -13.488 23.953 1 40.1 ? C6 UDP 402 B 1 HETATM 7 O O2 UDP . . . D 3 17.574 -16.429 21.98 1 31.63 ? O2 UDP 402 B 1 HETATM 8 O O4 UDP . . . D 3 14.235 -13.569 23.21 1 37.08 ? O4 UDP 402 B 1 HETATM 9 C C1' UDP . . . D 3 19.524 -15.031 23.283 1 33.77 ? C1' UDP 402 B 1 HETATM 10 C C2' UDP . . . D 3 20.45 -13.979 22.678 1 36.87 ? C2' UDP 402 B 1 HETATM 11 O O2' UDP . . . D 3 20.618 -14.28 21.312 1 40.42 ? O2' UDP 402 B 1 HETATM 12 C C3' UDP . . . D 3 21.742 -14.189 23.482 1 35.93 ? C3' UDP 402 B 1 HETATM 13 C C4' UDP . . . D 3 21.235 -14.675 24.852 1 34.83 ? C4' UDP 402 B 1 HETATM 14 O O4' UDP . . . D 3 19.9 -15.2 24.628 1 34.24 ? O4' UDP 402 B 1 HETATM 15 O O3' UDP . . . D 3 22.567 -15.144 22.83 1 42.21 ? O3' UDP 402 B 1 HETATM 16 C C5' UDP . . . D 3 21.151 -13.621 25.925 1 34.71 ? C5' UDP 402 B 1 HETATM 17 O O5' UDP . . . D 3 20.403 -12.512 25.396 1 36.53 ? O5' UDP 402 B 1 HETATM 18 P PA UDP . . . D 3 20.32 -11.082 26.138 1 40.07 ? PA UDP 402 B 1 HETATM 19 O O1A UDP . . . D 3 19.693 -10.143 25.15 1 32.74 ? O1A UDP 402 B 1 HETATM 20 O O2A UDP . . . D 3 19.685 -11.262 27.479 1 44.41 ? O2A UDP 402 B 1 HETATM 21 O O3A UDP . . . D 3 21.843 -10.729 26.458 1 42.29 ? O3A UDP 402 B 1 HETATM 22 P PB UDP . . . D 3 23.033 -9.994 25.658 1 64.3 ? PB UDP 402 B 1 HETATM 23 O O1B UDP . . . D 3 22.42 -9.389 24.419 1 61.11 ? O1B UDP 402 B 1 HETATM 24 O O2B UDP . . . D 3 23.982 -11.147 25.322 1 52.82 ? O2B UDP 402 B 1 HETATM 25 O O3B UDP . . . D 3 23.586 -8.926 26.667 1 58.12 ? O3B UDP 402 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #