data_8WOW # _model_server_result.job_id dbqtf9EMuS0BnJ1NnACuJw _model_server_result.datetime_utc '2024-11-26 14:03:12' _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 8wow # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8WOW # _exptl.entry_id 8WOW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 8WOW _cell.length_a 101.228 _cell.length_b 108.929 _cell.length_c 130.862 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WOW _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,I _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 ? 2 C N N ? 2 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 437 n n N1 C6 UDP sing 438 n n N1 C1' UDP sing 439 n n C2 N3 UDP sing 440 n n C2 O2 UDP doub 441 n n N3 C4 UDP sing 442 n n N3 HN3 UDP sing 443 n n C4 C5 UDP sing 444 n n C4 O4 UDP doub 445 n n C5 C6 UDP doub 446 n n C5 H5 UDP sing 447 n n C6 H6 UDP sing 448 n n C1' C2' UDP sing 449 n n C1' O4' UDP sing 450 n n C1' H1' UDP sing 451 n n C2' O2' UDP sing 452 n n C2' C3' UDP sing 453 n n C2' H2' UDP sing 454 n n O2' HO2' UDP sing 455 n n C3' C4' UDP sing 456 n n C3' O3' UDP sing 457 n n C3' H3' UDP sing 458 n n C4' O4' UDP sing 459 n n C4' C5' UDP sing 460 n n C4' H4' UDP sing 461 n n O3' HO3' UDP sing 462 n n C5' O5' UDP sing 463 n n C5' "H5'1" UDP sing 464 n n C5' "H5'2" UDP sing 465 n n O5' PA UDP sing 466 n n PA O1A UDP doub 467 n n PA O2A UDP sing 468 n n PA O3A UDP sing 469 n n O2A HOA2 UDP sing 470 n n O3A PB UDP sing 471 n n PB O1B UDP doub 472 n n PB O2B UDP sing 473 n n PB O3B UDP sing 474 n n O2B HOB2 UDP sing 475 n n O3B HOB3 UDP sing 476 n n # _atom_sites.entry_id 8WOW _atom_sites.fract_transf_matrix[1][1] 0.009879 _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] 0.00918 _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] 0.007642 _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 UDP A 1 401 401 UDP UDP . D 3 NAD A 1 402 400 NAD NAD . E 2 UDP B 1 401 401 UDP UDP . F 3 NAD B 1 402 400 NAD NAD . G 4 SO4 B 1 403 1 SO4 SO4 . H 5 HOH A 1 501 12 HOH HOH . H 5 HOH A 2 502 52 HOH HOH . H 5 HOH A 3 503 47 HOH HOH . H 5 HOH A 4 504 9 HOH HOH . H 5 HOH A 5 505 7 HOH HOH . H 5 HOH A 6 506 25 HOH HOH . H 5 HOH A 7 507 27 HOH HOH . H 5 HOH A 8 508 40 HOH HOH . H 5 HOH A 9 509 46 HOH HOH . H 5 HOH A 10 510 28 HOH HOH . H 5 HOH A 11 511 15 HOH HOH . H 5 HOH A 12 512 26 HOH HOH . H 5 HOH A 13 513 43 HOH HOH . H 5 HOH A 14 514 53 HOH HOH . H 5 HOH A 15 515 18 HOH HOH . H 5 HOH A 16 516 23 HOH HOH . H 5 HOH A 17 517 50 HOH HOH . H 5 HOH A 18 518 16 HOH HOH . H 5 HOH A 19 519 58 HOH HOH . H 5 HOH A 20 520 10 HOH HOH . H 5 HOH A 21 521 31 HOH HOH . H 5 HOH A 22 522 19 HOH HOH . H 5 HOH A 23 523 62 HOH HOH . H 5 HOH A 24 524 49 HOH HOH . H 5 HOH A 25 525 41 HOH HOH . H 5 HOH A 26 526 13 HOH HOH . H 5 HOH A 27 527 60 HOH HOH . H 5 HOH A 28 528 36 HOH HOH . H 5 HOH A 29 529 64 HOH HOH . H 5 HOH A 30 530 2 HOH HOH . I 5 HOH B 1 501 4 HOH HOH . I 5 HOH B 2 502 38 HOH HOH . I 5 HOH B 3 503 21 HOH HOH . I 5 HOH B 4 504 37 HOH HOH . I 5 HOH B 5 505 35 HOH HOH . I 5 HOH B 6 506 63 HOH HOH . I 5 HOH B 7 507 29 HOH HOH . I 5 HOH B 8 508 48 HOH HOH . I 5 HOH B 9 509 33 HOH HOH . I 5 HOH B 10 510 42 HOH HOH . I 5 HOH B 11 511 8 HOH HOH . I 5 HOH B 12 512 17 HOH HOH . I 5 HOH B 13 513 61 HOH HOH . I 5 HOH B 14 514 44 HOH HOH . I 5 HOH B 15 515 11 HOH HOH . I 5 HOH B 16 516 34 HOH HOH . I 5 HOH B 17 517 54 HOH HOH . I 5 HOH B 18 518 20 HOH HOH . I 5 HOH B 19 519 51 HOH HOH . I 5 HOH B 20 520 59 HOH HOH . I 5 HOH B 21 521 3 HOH HOH . I 5 HOH B 22 522 14 HOH HOH . I 5 HOH B 23 523 32 HOH HOH . I 5 HOH B 24 524 39 HOH HOH . I 5 HOH B 25 525 57 HOH HOH . I 5 HOH B 26 526 24 HOH HOH . I 5 HOH B 27 527 6 HOH HOH . I 5 HOH B 28 528 55 HOH HOH . I 5 HOH B 29 529 1 HOH HOH . I 5 HOH B 30 530 56 HOH HOH . I 5 HOH B 31 531 45 HOH HOH . I 5 HOH B 32 532 5 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 . . . E 2 49.063 23.7 13.385 1 27.9 ? N1 UDP 401 B 1 HETATM 2 C C2 UDP . . . E 2 50.125 24.301 14.051 1 27.4 ? C2 UDP 401 B 1 HETATM 3 N N3 UDP . . . E 2 49.825 25.461 14.72 1 24.82 ? N3 UDP 401 B 1 HETATM 4 C C4 UDP . . . E 2 48.597 26.075 14.799 1 25.27 ? C4 UDP 401 B 1 HETATM 5 C C5 UDP . . . E 2 47.55 25.404 14.078 1 24.52 ? C5 UDP 401 B 1 HETATM 6 C C6 UDP . . . E 2 47.807 24.256 13.432 1 24.85 ? C6 UDP 401 B 1 HETATM 7 O O2 UDP . . . E 2 51.25 23.821 14.082 1 24.95 ? O2 UDP 401 B 1 HETATM 8 O O4 UDP . . . E 2 48.491 27.108 15.464 1 24.41 ? O4 UDP 401 B 1 HETATM 9 C C1' UDP . . . E 2 49.356 22.438 12.634 1 29.86 ? C1' UDP 401 B 1 HETATM 10 C C2' UDP . . . E 2 48.59 21.219 13.149 1 31.82 ? C2' UDP 401 B 1 HETATM 11 O O2' UDP . . . E 2 49.328 20.69 14.235 1 33.55 ? O2' UDP 401 B 1 HETATM 12 C C3' UDP . . . E 2 48.58 20.351 11.88 1 29.69 ? C3' UDP 401 B 1 HETATM 13 C C4' UDP . . . E 2 48.397 21.378 10.748 1 27.85 ? C4' UDP 401 B 1 HETATM 14 O O4' UDP . . . E 2 49.014 22.585 11.265 1 29.47 ? O4' UDP 401 B 1 HETATM 15 O O3' UDP . . . E 2 49.829 19.692 11.744 1 29.5 ? O3' UDP 401 B 1 HETATM 16 C C5' UDP . . . E 2 46.973 21.691 10.362 1 27.6 ? C5' UDP 401 B 1 HETATM 17 O O5' UDP . . . E 2 46.208 21.744 11.601 1 27.62 ? O5' UDP 401 B 1 HETATM 18 P PA UDP . . . E 2 44.757 22.351 11.745 1 25.15 ? PA UDP 401 B 1 HETATM 19 O O1A UDP . . . E 2 44.566 23.495 10.81 1 31.38 ? O1A UDP 401 B 1 HETATM 20 O O2A UDP . . . E 2 44.375 22.54 13.172 1 31.1 ? O2A UDP 401 B 1 HETATM 21 O O3A UDP . . . E 2 43.932 21.124 11.207 1 32.52 ? O3A UDP 401 B 1 HETATM 22 P PB UDP . . . E 2 43.805 19.572 11.581 1 41.68 ? PB UDP 401 B 1 HETATM 23 O O1B UDP . . . E 2 44.906 18.91 10.75 1 38.14 ? O1B UDP 401 B 1 HETATM 24 O O2B UDP . . . E 2 42.39 19.227 11.099 1 33.62 ? O2B UDP 401 B 1 HETATM 25 O O3B UDP . . . E 2 43.999 19.41 13.078 1 38.94 ? O3B UDP 401 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #