data_7C1Y # _model_server_result.job_id wyp-k5CLRyKt0RVDtWaJ7g _model_server_result.datetime_utc '2024-10-20 08:08:54' _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 7c1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 7C1Y # _exptl.entry_id 7C1Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 3 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.515 _cell.angle_gamma 90 _cell.entry_id 7C1Y _cell.length_a 79.328 _cell.length_b 48.857 _cell.length_c 91.788 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7C1Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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,J _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 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 45 A CYS 45 1_555 A SG CYS 312 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 45 B CYS 45 1_555 B SG CYS 312 B CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A O LYS 305 A LYS 305 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc2 A O ALA 341 A ALA 341 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc3 A O SER 344 A SER 344 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc4 A O ASP 346 A ASP 346 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc5 B O LYS 305 B LYS 305 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc6 B O ALA 341 B ALA 341 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc7 B O SER 344 B SER 344 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc8 B O ASP 346 B ASP 346 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? # _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 ? # _atom_sites.entry_id 7C1Y _atom_sites.fract_transf_matrix[1][1] 0.012606 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003978 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020468 _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] 0.011424 _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 NA A 1 401 1 NA NA . D 3 FJF A 1 402 1 FJF PUD . E 4 ADP A 1 403 1 ADP ADP . F 2 NA B 1 401 2 NA NA . G 3 FJF B 1 402 2 FJF PUD . H 4 ADP B 1 403 2 ADP ADP . I 5 HOH A 1 501 83 HOH HOH . I 5 HOH A 2 502 58 HOH HOH . I 5 HOH A 3 503 82 HOH HOH . I 5 HOH A 4 504 39 HOH HOH . I 5 HOH A 5 505 6 HOH HOH . I 5 HOH A 6 506 75 HOH HOH . I 5 HOH A 7 507 1 HOH HOH . I 5 HOH A 8 508 31 HOH HOH . I 5 HOH A 9 509 3 HOH HOH . I 5 HOH A 10 510 29 HOH HOH . I 5 HOH A 11 511 32 HOH HOH . I 5 HOH A 12 512 42 HOH HOH . I 5 HOH A 13 513 28 HOH HOH . I 5 HOH A 14 514 4 HOH HOH . I 5 HOH A 15 515 16 HOH HOH . I 5 HOH A 16 516 15 HOH HOH . I 5 HOH A 17 517 7 HOH HOH . I 5 HOH A 18 518 74 HOH HOH . I 5 HOH A 19 519 21 HOH HOH . I 5 HOH A 20 520 41 HOH HOH . I 5 HOH A 21 521 77 HOH HOH . I 5 HOH A 22 522 37 HOH HOH . I 5 HOH A 23 523 50 HOH HOH . I 5 HOH A 24 524 69 HOH HOH . I 5 HOH A 25 525 2 HOH HOH . I 5 HOH A 26 526 35 HOH HOH . I 5 HOH A 27 527 53 HOH HOH . I 5 HOH A 28 528 25 HOH HOH . I 5 HOH A 29 529 76 HOH HOH . I 5 HOH A 30 530 23 HOH HOH . I 5 HOH A 31 531 33 HOH HOH . I 5 HOH A 32 532 49 HOH HOH . I 5 HOH A 33 533 59 HOH HOH . I 5 HOH A 34 534 26 HOH HOH . I 5 HOH A 35 535 13 HOH HOH . I 5 HOH A 36 536 73 HOH HOH . I 5 HOH A 37 537 36 HOH HOH . I 5 HOH A 38 538 78 HOH HOH . I 5 HOH A 39 539 20 HOH HOH . I 5 HOH A 40 540 27 HOH HOH . I 5 HOH A 41 541 9 HOH HOH . I 5 HOH A 42 542 67 HOH HOH . I 5 HOH A 43 543 43 HOH HOH . I 5 HOH A 44 544 72 HOH HOH . I 5 HOH A 45 545 19 HOH HOH . I 5 HOH A 46 546 56 HOH HOH . I 5 HOH A 47 547 57 HOH HOH . I 5 HOH A 48 548 51 HOH HOH . I 5 HOH A 49 549 79 HOH HOH . I 5 HOH A 50 550 55 HOH HOH . I 5 HOH A 51 551 61 HOH HOH . I 5 HOH A 52 552 68 HOH HOH . I 5 HOH A 53 553 70 HOH HOH . J 5 HOH B 1 501 80 HOH HOH . J 5 HOH B 2 502 66 HOH HOH . J 5 HOH B 3 503 81 HOH HOH . J 5 HOH B 4 504 64 HOH HOH . J 5 HOH B 5 505 62 HOH HOH . J 5 HOH B 6 506 5 HOH HOH . J 5 HOH B 7 507 10 HOH HOH . J 5 HOH B 8 508 40 HOH HOH . J 5 HOH B 9 509 44 HOH HOH . J 5 HOH B 10 510 8 HOH HOH . J 5 HOH B 11 511 14 HOH HOH . J 5 HOH B 12 512 47 HOH HOH . J 5 HOH B 13 513 48 HOH HOH . J 5 HOH B 14 514 71 HOH HOH . J 5 HOH B 15 515 46 HOH HOH . J 5 HOH B 16 516 12 HOH HOH . J 5 HOH B 17 517 45 HOH HOH . J 5 HOH B 18 518 63 HOH HOH . J 5 HOH B 19 519 38 HOH HOH . J 5 HOH B 20 520 11 HOH HOH . J 5 HOH B 21 521 18 HOH HOH . J 5 HOH B 22 522 24 HOH HOH . J 5 HOH B 23 523 30 HOH HOH . J 5 HOH B 24 524 22 HOH HOH . J 5 HOH B 25 525 60 HOH HOH . J 5 HOH B 26 526 34 HOH HOH . J 5 HOH B 27 527 54 HOH HOH . J 5 HOH B 28 528 65 HOH HOH . J 5 HOH B 29 529 17 HOH HOH . J 5 HOH B 30 530 52 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 . . . D 3 11.352 -7.294 47.166 1 31.15 ? O01 FJF 402 A 1 HETATM 2 C C02 FJF . . . D 3 10.381 -7.983 46.903 1 31.38 ? C02 FJF 402 A 1 HETATM 3 N N03 FJF . . . D 3 9.061 -7.399 46.69 1 37.83 ? N03 FJF 402 A 1 HETATM 4 C C04 FJF . . . D 3 7.944 -8.212 46.352 1 30.3 ? C04 FJF 402 A 1 HETATM 5 C C05 FJF . . . D 3 8.095 -9.658 46.227 1 30.12 ? C05 FJF 402 A 1 HETATM 6 C C06 FJF . . . D 3 9.429 -10.233 46.433 1 32.06 ? C06 FJF 402 A 1 HETATM 7 O O07 FJF . . . D 3 9.594 -11.427 46.33 1 37.45 ? O07 FJF 402 A 1 HETATM 8 N N08 FJF . . . D 3 10.53 -9.41 46.77 1 31.1 ? N08 FJF 402 A 1 HETATM 9 C C09 FJF . . . D 3 6.924 -10.558 45.874 1 25.7 ? C09 FJF 402 A 1 HETATM 10 O O10 FJF . . . D 3 6.334 -10.126 44.829 1 31.35 ? O10 FJF 402 A 1 HETATM 11 C C11 FJF . . . D 3 5.006 -11.031 44.896 1 38.56 ? C11 FJF 402 A 1 HETATM 12 C C12 FJF . . . D 3 4.026 -10.62 43.797 1 41.95 ? C12 FJF 402 A 1 HETATM 13 O O13 FJF . . . D 3 4.696 -10.588 42.543 1 37.62 ? O13 FJF 402 A 1 HETATM 14 C C14 FJF . . . D 3 4.546 -10.851 46.084 1 34.9 ? C14 FJF 402 A 1 HETATM 15 O O15 FJF . . . D 3 3.913 -12.122 46.637 1 31.27 ? O15 FJF 402 A 1 HETATM 16 C C16 FJF . . . D 3 5.76 -10.472 46.92 1 36.02 ? C16 FJF 402 A 1 HETATM 17 O O17 FJF . . . D 3 5.923 -11.324 47.983 1 35.87 ? O17 FJF 402 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #