data_7VSK # _model_server_result.job_id Y2N2BVpflkqKoWsIdVJvyw _model_server_result.datetime_utc '2024-12-03 18:30:12' _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 7vsk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7VSK # _exptl.entry_id 7VSK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione _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 120 _cell.entry_id 7VSK _cell.length_a 182.634 _cell.length_b 182.634 _cell.length_c 51.228 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VSK _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall 'P 6c 2c' _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id FJF _chem_comp.mon_nstd_flag . _chem_comp.name 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione _chem_comp.type non-polymer _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 O13 C12 FJF sing 83 n n C12 C11 FJF sing 84 n n O10 C11 FJF sing 85 n n O10 C09 FJF sing 86 n n C11 C14 FJF sing 87 n n C09 C05 FJF sing 88 n n C09 C16 FJF sing 89 n n C14 O15 FJF sing 90 n n C14 C16 FJF sing 91 n n C05 C04 FJF doub 92 n n C05 C06 FJF sing 93 n n O07 C06 FJF doub 94 n n C04 N03 FJF sing 95 n n C06 N08 FJF sing 96 n n N03 C02 FJF sing 97 n n N08 C02 FJF sing 98 n n C02 O01 FJF doub 99 n n C16 O17 FJF sing 100 n n C04 H1 FJF sing 101 n n N08 H3 FJF sing 102 n n C09 H4 FJF sing 103 n n C11 H5 FJF sing 104 n n C12 H6 FJF sing 105 n n C12 H7 FJF sing 106 n n O13 H8 FJF sing 107 n n C14 H9 FJF sing 108 n n O15 H10 FJF sing 109 n n C16 H11 FJF sing 110 n n O17 H12 FJF sing 111 n n N03 H13 FJF sing 112 n n # _atom_sites.entry_id 7VSK _atom_sites.fract_transf_matrix[1][1] 0.005475 _atom_sites.fract_transf_matrix[1][2] 0.003161 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006322 _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] 0.019521 _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 FJF A 1 401 301 FJF PSU . C 3 HOH A 1 501 22 HOH HOH . C 3 HOH A 2 502 52 HOH HOH . C 3 HOH A 3 503 49 HOH HOH . C 3 HOH A 4 504 43 HOH HOH . C 3 HOH A 5 505 41 HOH HOH . C 3 HOH A 6 506 72 HOH HOH . C 3 HOH A 7 507 35 HOH HOH . C 3 HOH A 8 508 30 HOH HOH . C 3 HOH A 9 509 20 HOH HOH . C 3 HOH A 10 510 67 HOH HOH . C 3 HOH A 11 511 42 HOH HOH . C 3 HOH A 12 512 3 HOH HOH . C 3 HOH A 13 513 65 HOH HOH . C 3 HOH A 14 514 48 HOH HOH . C 3 HOH A 15 515 21 HOH HOH . C 3 HOH A 16 516 54 HOH HOH . C 3 HOH A 17 517 4 HOH HOH . C 3 HOH A 18 518 9 HOH HOH . C 3 HOH A 19 519 27 HOH HOH . C 3 HOH A 20 520 50 HOH HOH . C 3 HOH A 21 521 40 HOH HOH . C 3 HOH A 22 522 7 HOH HOH . C 3 HOH A 23 523 38 HOH HOH . C 3 HOH A 24 524 2 HOH HOH . C 3 HOH A 25 525 1 HOH HOH . C 3 HOH A 26 526 36 HOH HOH . C 3 HOH A 27 527 74 HOH HOH . C 3 HOH A 28 528 32 HOH HOH . C 3 HOH A 29 529 10 HOH HOH . C 3 HOH A 30 530 13 HOH HOH . C 3 HOH A 31 531 23 HOH HOH . C 3 HOH A 32 532 39 HOH HOH . C 3 HOH A 33 533 64 HOH HOH . C 3 HOH A 34 534 29 HOH HOH . C 3 HOH A 35 535 5 HOH HOH . C 3 HOH A 36 536 17 HOH HOH . C 3 HOH A 37 537 18 HOH HOH . C 3 HOH A 38 538 73 HOH HOH . C 3 HOH A 39 539 46 HOH HOH . C 3 HOH A 40 540 69 HOH HOH . C 3 HOH A 41 541 63 HOH HOH . C 3 HOH A 42 542 16 HOH HOH . C 3 HOH A 43 543 61 HOH HOH . C 3 HOH A 44 544 37 HOH HOH . C 3 HOH A 45 545 24 HOH HOH . C 3 HOH A 46 546 11 HOH HOH . C 3 HOH A 47 547 45 HOH HOH . C 3 HOH A 48 548 60 HOH HOH . C 3 HOH A 49 549 15 HOH HOH . C 3 HOH A 50 550 53 HOH HOH . C 3 HOH A 51 551 28 HOH HOH . C 3 HOH A 52 552 6 HOH HOH . C 3 HOH A 53 553 12 HOH HOH . C 3 HOH A 54 554 66 HOH HOH . C 3 HOH A 55 555 8 HOH HOH . C 3 HOH A 56 556 59 HOH HOH . C 3 HOH A 57 557 44 HOH HOH . C 3 HOH A 58 558 31 HOH HOH . C 3 HOH A 59 559 33 HOH HOH . C 3 HOH A 60 560 71 HOH HOH . C 3 HOH A 61 561 55 HOH HOH . C 3 HOH A 62 562 70 HOH HOH . C 3 HOH A 63 563 26 HOH HOH . C 3 HOH A 64 564 34 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 O O01 FJF . . . B 2 76.378 -25.929 -11.847 1 38.9 ? O01 FJF 401 A 1 HETATM 2 C C02 FJF . . . B 2 75.497 -26.099 -10.992 1 42.93 ? C02 FJF 401 A 1 HETATM 3 N N03 FJF . . . B 2 75.431 -27.285 -10.266 1 48.46 ? N03 FJF 401 A 1 HETATM 4 C C04 FJF . . . B 2 74.479 -27.497 -9.32 1 45.54 ? C04 FJF 401 A 1 HETATM 5 C C05 FJF . . . B 2 73.548 -26.499 -9.065 1 41.63 ? C05 FJF 401 A 1 HETATM 6 C C06 FJF . . . B 2 73.591 -25.307 -9.794 1 41.26 ? C06 FJF 401 A 1 HETATM 7 O O07 FJF . . . B 2 72.769 -24.422 -9.571 1 38.62 ? O07 FJF 401 A 1 HETATM 8 N N08 FJF . . . B 2 74.568 -25.1 -10.751 1 41.36 ? N08 FJF 401 A 1 HETATM 9 C C09 FJF . . . B 2 72.474 -26.68 -8.033 1 43.06 ? C09 FJF 401 A 1 HETATM 10 O O10 FJF . . . B 2 72.936 -26.338 -6.75 1 43.75 ? O10 FJF 401 A 1 HETATM 11 C C11 FJF . . . B 2 72.199 -27.086 -5.757 1 42.48 ? C11 FJF 401 A 1 HETATM 12 C C12 FJF . . . B 2 73.139 -27.424 -4.627 1 46.56 ? C12 FJF 401 A 1 HETATM 13 O O13 FJF . . . B 2 73.541 -26.244 -3.925 1 47.78 ? O13 FJF 401 A 1 HETATM 14 C C14 FJF . . . B 2 71.587 -28.292 -6.481 1 44.22 ? C14 FJF 401 A 1 HETATM 15 O O15 FJF . . . B 2 70.168 -28.202 -6.417 1 43.61 ? O15 FJF 401 A 1 HETATM 16 C C16 FJF . . . B 2 72.005 -28.13 -7.952 1 44.08 ? C16 FJF 401 A 1 HETATM 17 O O17 FJF . . . B 2 70.944 -28.359 -8.856 1 40.42 ? O17 FJF 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #