data_7F2A # _model_server_result.job_id vatu7nPrEgi3h1RIej1-sA _model_server_result.datetime_utc '2024-11-23 23:21:43' _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 7f2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 7F2A # _exptl.entry_id 7F2A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 7F2A _cell.length_a 48.855 _cell.length_b 125.287 _cell.length_c 128.278 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7F2A _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,I 1 1 B,G,H,J 2 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 G N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 158 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 158 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 158 _struct_conn.ptnr2_auth_asym_id F _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 158 _struct_conn.ptnr2_symmetry 2_454 _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 1.964 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 338 n n PA O2A TYD sing 339 n n PA O3A TYD sing 340 n n PA O5' TYD sing 341 n n O2A HOA2 TYD sing 342 n n O3A PB TYD sing 343 n n PB O1B TYD doub 344 n n PB O2B TYD sing 345 n n PB O3B TYD sing 346 n n O2B HOB2 TYD sing 347 n n O3B HOB3 TYD sing 348 n n O5' C5' TYD sing 349 n n C5' C4' TYD sing 350 n n C5' "H5'1" TYD sing 351 n n C5' "H5'2" TYD sing 352 n n C4' O4' TYD sing 353 n n C4' C3' TYD sing 354 n n C4' H4' TYD sing 355 n n O4' C1' TYD sing 356 n n C3' O3' TYD sing 357 n n C3' C2' TYD sing 358 n n C3' H3' TYD sing 359 n n O3' HO3' TYD sing 360 n n C2' C1' TYD sing 361 n n C2' "H2'1" TYD sing 362 n n C2' "H2'2" TYD sing 363 n n C1' N1 TYD sing 364 n n C1' H1' TYD sing 365 n n N1 C2 TYD sing 366 n y N1 C6 TYD sing 367 n y C2 O2 TYD doub 368 n n C2 N3 TYD sing 369 n y N3 C4 TYD sing 370 n y N3 HN3 TYD sing 371 n n C4 O4 TYD doub 372 n n C4 C5 TYD sing 373 n y C5 C5M TYD sing 374 n n C5 C6 TYD doub 375 n y C5M H51 TYD sing 376 n n C5M H52 TYD sing 377 n n C5M H53 TYD sing 378 n n C6 H6 TYD sing 379 n n # _atom_sites.entry_id 7F2A _atom_sites.fract_transf_matrix[1][1] 0.020469 _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] 0.007982 _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] 0.007796 _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 TYD A 1 401 401 TYD TYD . D 3 SO4 A 1 402 1 SO4 SO4 . E 3 SO4 A 1 403 2 SO4 SO4 . F 3 SO4 A 1 404 3 SO4 SO4 . G 2 TYD F 1 401 401 TYD TYD . H 3 SO4 F 1 402 4 SO4 SO4 . I 4 HOH A 1 501 5 HOH HOH . I 4 HOH A 2 502 2 HOH HOH . J 4 HOH F 1 501 3 HOH HOH . J 4 HOH F 2 502 10 HOH HOH . J 4 HOH F 3 503 4 HOH HOH . J 4 HOH F 4 504 6 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 PA TYD . . . C 2 5.395 -13.922 -14.413 1 42.73 ? PA TYD 401 A 1 HETATM 2 O O1A TYD . . . C 2 5.097 -15.354 -14.829 1 38.23 ? O1A TYD 401 A 1 HETATM 3 O O2A TYD . . . C 2 4.15 -13.232 -14.167 1 35.43 ? O2A TYD 401 A 1 HETATM 4 O O3A TYD . . . C 2 6.255 -13.94 -13.023 1 42.76 ? O3A TYD 401 A 1 HETATM 5 P PB TYD . . . C 2 7.729 -13.398 -12.806 1 35.74 ? PB TYD 401 A 1 HETATM 6 O O1B TYD . . . C 2 8.541 -13.311 -14.046 1 44.2 ? O1B TYD 401 A 1 HETATM 7 O O2B TYD . . . C 2 8.435 -14.323 -11.886 1 40.7 ? O2B TYD 401 A 1 HETATM 8 O O3B TYD . . . C 2 7.623 -12.091 -12.148 1 37.31 ? O3B TYD 401 A 1 HETATM 9 O O5' TYD . . . C 2 6.262 -13.171 -15.597 1 40.06 ? O5' TYD 401 A 1 HETATM 10 C C5' TYD . . . C 2 6.602 -13.958 -16.713 1 38.78 ? C5' TYD 401 A 1 HETATM 11 C C4' TYD . . . C 2 6.481 -13.131 -17.946 1 38.82 ? C4' TYD 401 A 1 HETATM 12 O O4' TYD . . . C 2 7.434 -13.415 -18.735 1 40.19 ? O4' TYD 401 A 1 HETATM 13 C C3' TYD . . . C 2 5.058 -13.577 -18.673 1 37.13 ? C3' TYD 401 A 1 HETATM 14 O O3' TYD . . . C 2 4.421 -12.387 -19.207 1 36.84 ? O3' TYD 401 A 1 HETATM 15 C C2' TYD . . . C 2 5.366 -14.361 -19.571 1 40.9 ? C2' TYD 401 A 1 HETATM 16 C C1' TYD . . . C 2 6.761 -13.812 -20.035 1 41.87 ? C1' TYD 401 A 1 HETATM 17 N N1 TYD . . . C 2 7.497 -14.734 -20.684 1 42.98 ? N1 TYD 401 A 1 HETATM 18 C C2 TYD . . . C 2 7.751 -14.544 -22.009 1 39.63 ? C2 TYD 401 A 1 HETATM 19 O O2 TYD . . . C 2 7.327 -13.603 -22.55 1 41.04 ? O2 TYD 401 A 1 HETATM 20 N N3 TYD . . . C 2 8.494 -15.438 -22.698 1 39.82 ? N3 TYD 401 A 1 HETATM 21 C C4 TYD . . . C 2 8.978 -16.495 -22.105 1 41.55 ? C4 TYD 401 A 1 HETATM 22 O O4 TYD . . . C 2 9.616 -17.254 -22.692 1 43.41 ? O4 TYD 401 A 1 HETATM 23 C C5 TYD . . . C 2 8.735 -16.697 -20.771 1 40.46 ? C5 TYD 401 A 1 HETATM 24 C C5M TYD . . . C 2 9.304 -17.909 -20.122 1 33.05 ? C5M TYD 401 A 1 HETATM 25 C C6 TYD . . . C 2 7.987 -15.798 -20.064 1 42.46 ? C6 TYD 401 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #