data_4TKR # _model_server_result.job_id XKX6b0tJGShtTW5yD7Zlkg _model_server_result.datetime_utc '2024-12-22 05:45:56' _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 4tkr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 4TKR # _exptl.entry_id 4TKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMINE 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 120 _cell.entry_id 4TKR _cell.length_a 95.647 _cell.length_b 95.647 _cell.length_c 125.027 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 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,K,L,M,N,O,P,Q,R,S _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 J N N # _chem_comp.formula 'C12 H19 N4 O7 P2 S 1' _chem_comp.formula_weight 425.314 _chem_comp.id TPP _chem_comp.mon_nstd_flag . _chem_comp.name 'THIAMINE 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 N1' C2' TPP doub 352 n y N1' C6' TPP sing 353 n y C2' CM2 TPP sing 354 n n C2' N3' TPP sing 355 n y CM2 HM21 TPP sing 356 n n CM2 HM22 TPP sing 357 n n CM2 HM23 TPP sing 358 n n N3' C4' TPP doub 359 n y C4' N4' TPP sing 360 n n C4' C5' TPP sing 361 n y N4' HN41 TPP sing 362 n n N4' HN42 TPP sing 363 n n C5' C6' TPP doub 364 n y C5' C7' TPP sing 365 n n C6' H6' TPP sing 366 n n C7' N3 TPP sing 367 n n C7' "H7'1" TPP sing 368 n n C7' "H7'2" TPP sing 369 n n N3 C2 TPP doub 370 n y N3 C4 TPP sing 371 n y C2 S1 TPP sing 372 n y C2 H2 TPP sing 373 n n S1 C5 TPP sing 374 n y C5 C4 TPP doub 375 n y C5 C6 TPP sing 376 n n C4 CM4 TPP sing 377 n n CM4 HM41 TPP sing 378 n n CM4 HM42 TPP sing 379 n n CM4 HM43 TPP sing 380 n n C6 C7 TPP sing 381 n n C6 H61 TPP sing 382 n n C6 H62 TPP sing 383 n n C7 O7 TPP sing 384 n n C7 H71 TPP sing 385 n n C7 H72 TPP sing 386 n n O7 PA TPP sing 387 n n PA O1A TPP doub 388 n n PA O2A TPP sing 389 n n PA O3A TPP sing 390 n n O2A HOA2 TPP sing 391 n n O3A PB TPP sing 392 n n PB O1B TPP doub 393 n n PB O2B TPP sing 394 n n PB O3B TPP sing 395 n n O2B HOB2 TPP sing 396 n n O3B HOB3 TPP sing 397 n n # _atom_sites.entry_id 4TKR _atom_sites.fract_transf_matrix[1][1] 0.010455 _atom_sites.fract_transf_matrix[1][2] 0.006036 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012073 _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] 0.007998 _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 TPP A 1 301 301 TPP TPP . D 3 BGL A 1 302 302 BGL BGL . E 3 BGL A 1 303 303 BGL BGL . F 3 BGL A 1 304 304 BGL BGL . G 3 BGL A 1 305 305 BGL BGL . H 3 BGL A 1 306 306 BGL BGL . I 3 BGL A 1 307 307 BGL BGL . J 2 TPP B 1 301 301 TPP TPP . K 3 BGL B 1 302 302 BGL BGL . L 3 BGL B 1 303 303 BGL BGL . M 3 BGL B 1 304 304 BGL BGL . N 3 BGL B 1 305 305 BGL BGL . O 3 BGL B 1 306 306 BGL BGL . P 3 BGL B 1 307 307 BGL BGL . Q 3 BGL B 1 308 308 BGL BGL . R 3 BGL B 1 309 309 BGL BGL . S 3 BGL B 1 310 310 BGL BGL . # 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' TPP . . . J 2 -17.947 29.534 35.928 1 52.34 ? N1' TPP 301 B 1 HETATM 2 C C2' TPP . . . J 2 -17.125 30.398 35.235 1 59.31 ? C2' TPP 301 B 1 HETATM 3 C CM2 TPP . . . J 2 -17.696 31.257 34.146 1 59.68 ? CM2 TPP 301 B 1 HETATM 4 N N3' TPP . . . J 2 -15.781 30.473 35.544 1 56.68 ? N3' TPP 301 B 1 HETATM 5 C C4' TPP . . . J 2 -15.25 29.683 36.544 1 48.29 ? C4' TPP 301 B 1 HETATM 6 N N4' TPP . . . J 2 -13.955 29.765 36.834 1 48.31 ? N4' TPP 301 B 1 HETATM 7 C C5' TPP . . . J 2 -16.076 28.819 37.254 1 53.06 ? C5' TPP 301 B 1 HETATM 8 C C6' TPP . . . J 2 -17.426 28.744 36.932 1 55.41 ? C6' TPP 301 B 1 HETATM 9 C C7' TPP . . . J 2 -15.531 27.929 38.349 1 55.58 ? C7' TPP 301 B 1 HETATM 10 N N3 TPP . . . J 2 -15.145 28.647 39.536 1 51.58 ? N3 TPP 301 B 1 HETATM 11 C C2 TPP . . . J 2 -15.487 29.945 39.834 1 51.56 ? C2 TPP 301 B 1 HETATM 12 S S1 TPP . . . J 2 -14.901 30.437 41.237 1 42.92 ? S1 TPP 301 B 1 HETATM 13 C C5 TPP . . . J 2 -14.219 29.029 41.53 1 46.55 ? C5 TPP 301 B 1 HETATM 14 C C4 TPP . . . J 2 -14.41 28.097 40.527 1 43.86 ? C4 TPP 301 B 1 HETATM 15 C CM4 TPP . . . J 2 -13.877 26.695 40.538 1 41.66 ? CM4 TPP 301 B 1 HETATM 16 C C6 TPP . . . J 2 -13.481 28.951 42.834 1 50.39 ? C6 TPP 301 B 1 HETATM 17 C C7 TPP . . . J 2 -14.409 28.369 43.891 1 57.45 ? C7 TPP 301 B 1 HETATM 18 O O7 TPP . . . J 2 -15.384 29.338 44.202 1 62.1 ? O7 TPP 301 B 1 HETATM 19 P PA TPP . . . J 2 -16.532 29.045 45.289 1 76.29 ? PA TPP 301 B 1 HETATM 20 O O1A TPP . . . J 2 -17.677 28.317 44.626 1 73.09 ? O1A TPP 301 B 1 HETATM 21 O O2A TPP . . . J 2 -17 30.33 45.929 1 71.29 ? O2A TPP 301 B 1 HETATM 22 O O3A TPP . . . J 2 -15.817 28.066 46.35 1 188.81 ? O3A TPP 301 B 1 HETATM 23 P PB TPP . . . J 2 -15.247 28.616 47.752 1 57.47 ? PB TPP 301 B 1 HETATM 24 O O1B TPP . . . J 2 -14.727 30.022 47.569 1 51.27 ? O1B TPP 301 B 1 HETATM 25 O O2B TPP . . . J 2 -16.352 28.616 48.781 1 74.43 ? O2B TPP 301 B 1 HETATM 26 O O3B TPP . . . J 2 -14.126 27.721 48.222 1 60.14 ? O3B TPP 301 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #