data_2PDA # _model_server_result.job_id aMB7dfYxLGwCLDQZTLvoDQ _model_server_result.datetime_utc '2024-12-22 02:56:38' _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 2pda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1243}' # _entry.id 2PDA # _exptl.entry_id 2PDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 5 _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 90 _cell.entry_id 2PDA _cell.length_a 86 _cell.length_b 146.3 _cell.length_c 211.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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 ? 5 H N N ? 5 O 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 1194 A CYS 1195 1_555 A SG CYS 1211 A CYS 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 1194 B CYS 1195 1_555 B SG CYS 1211 B CYS 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A SG CYS 688 A CYS 689 1_555 E FE1 SF4 . A SF4 1233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc2 A SG CYS 691 A CYS 692 1_555 E FE2 SF4 . A SF4 1233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc3 A SG CYS 694 A CYS 695 1_555 E FE3 SF4 . A SF4 1233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc4 A SG CYS 698 A CYS 699 1_555 F FE1 SF4 . A SF4 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc5 A SG CYS 744 A CYS 745 1_555 F FE2 SF4 . A SF4 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc6 A SG CYS 747 A CYS 748 1_555 F FE4 SF4 . A SF4 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc7 A SG CYS 750 A CYS 751 1_555 F FE3 SF4 . A SF4 1234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc8 A SG CYS 754 A CYS 755 1_555 E FE4 SF4 . A SF4 1233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc9 A SG CYS 811 A CYS 812 1_555 G FE1 SF4 . A SF4 1235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc10 A SG CYS 814 A CYS 815 1_555 G FE2 SF4 . A SF4 1235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc11 A SG CYS 839 A CYS 840 1_555 G FE3 SF4 . A SF4 1235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc12 A OD1 ASP 962 A ASP 963 1_555 C MG MG . A MG 1237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc13 A OD1 ASP 982 A ASP 983 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc14 A OD1 ASN 984 A ASN 985 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc15 A O VAL 992 A VAL 993 1_555 C MG MG . A MG 1237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc16 A O ALA 1055 A ALA 1056 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc17 A O PHE 1058 A PHE 1059 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc18 A O GLY 1060 A GLY 1061 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc19 A OG SER 1062 A SER 1063 1_555 D CA CA . A CA 1238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc20 A SG CYS 1070 A CYS 1071 1_555 G FE4 SF4 . A SF4 1235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc21 H O1B TPP . A TPP 1236 1_555 C MG MG . A MG 1237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc22 B SG CYS 688 B CYS 689 1_555 L FE1 SF4 . B SF4 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc23 B SG CYS 691 B CYS 692 1_555 L FE2 SF4 . B SF4 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc24 B SG CYS 694 B CYS 695 1_555 L FE3 SF4 . B SF4 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc25 B SG CYS 698 B CYS 699 1_555 M FE1 SF4 . B SF4 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc26 B SG CYS 744 B CYS 745 1_555 M FE2 SF4 . B SF4 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc27 B SG CYS 747 B CYS 748 1_555 M FE4 SF4 . B SF4 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc28 B SG CYS 750 B CYS 751 1_555 M FE3 SF4 . B SF4 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc29 B SG CYS 754 B CYS 755 1_555 L FE4 SF4 . B SF4 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc30 B SG CYS 811 B CYS 812 1_555 N FE1 SF4 . B SF4 1242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc31 B SG CYS 814 B CYS 815 1_555 N FE2 SF4 . B SF4 1242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc32 B SG CYS 839 B CYS 840 1_555 N FE3 SF4 . B SF4 1242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc33 B OD1 ASP 962 B ASP 963 1_555 J MG MG . B MG 1244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc34 B OD1 ASP 982 B ASP 983 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc35 B OD1 ASN 984 B ASN 985 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc36 B O VAL 992 B VAL 993 1_555 J MG MG . B MG 1244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc37 B O ALA 1055 B ALA 1056 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc38 B O PHE 1058 B PHE 1059 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc39 B O GLY 1060 B GLY 1061 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc40 B OG SER 1062 B SER 1063 1_555 K CA CA . B CA 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc41 B SG CYS 1070 B CYS 1071 1_555 N FE4 SF4 . B SF4 1242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc42 O O1B TPP . B TPP 1243 1_555 J MG MG . B MG 1244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? # _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 327 n y N1' C6' TPP sing 328 n y C2' CM2 TPP sing 329 n n C2' N3' TPP sing 330 n y CM2 HM21 TPP sing 331 n n CM2 HM22 TPP sing 332 n n CM2 HM23 TPP sing 333 n n N3' C4' TPP doub 334 n y C4' N4' TPP sing 335 n n C4' C5' TPP sing 336 n y N4' HN41 TPP sing 337 n n N4' HN42 TPP sing 338 n n C5' C6' TPP doub 339 n y C5' C7' TPP sing 340 n n C6' H6' TPP sing 341 n n C7' N3 TPP sing 342 n n C7' "H7'1" TPP sing 343 n n C7' "H7'2" TPP sing 344 n n N3 C2 TPP doub 345 n y N3 C4 TPP sing 346 n y C2 S1 TPP sing 347 n y C2 H2 TPP sing 348 n n S1 C5 TPP sing 349 n y C5 C4 TPP doub 350 n y C5 C6 TPP sing 351 n n C4 CM4 TPP sing 352 n n CM4 HM41 TPP sing 353 n n CM4 HM42 TPP sing 354 n n CM4 HM43 TPP sing 355 n n C6 C7 TPP sing 356 n n C6 H61 TPP sing 357 n n C6 H62 TPP sing 358 n n C7 O7 TPP sing 359 n n C7 H71 TPP sing 360 n n C7 H72 TPP sing 361 n n O7 PA TPP sing 362 n n PA O1A TPP doub 363 n n PA O2A TPP sing 364 n n PA O3A TPP sing 365 n n O2A HOA2 TPP sing 366 n n O3A PB TPP sing 367 n n PB O1B TPP doub 368 n n PB O2B TPP sing 369 n n PB O3B TPP sing 370 n n O2B HOB2 TPP sing 371 n n O3B HOB3 TPP sing 372 n n # _atom_sites.entry_id 2PDA _atom_sites.fract_transf_matrix[1][1] 0.011628 _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] 0.006835 _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] 0.004719 _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 MG A 1 1237 1237 MG MG . D 3 CA A 1 1238 1238 CA CA . E 4 SF4 A 1 1233 1233 SF4 FS4 . F 4 SF4 A 1 1234 1234 SF4 FS4 . G 4 SF4 A 1 1235 1235 SF4 FS4 . H 5 TPP A 1 1236 1236 TPP TPP . I 6 PYR A 1 1239 1239 PYR PYR . J 2 MG B 1 1244 1244 MG MG . K 3 CA B 1 1245 1245 CA CA . L 4 SF4 B 1 1240 1240 SF4 FS4 . M 4 SF4 B 1 1241 1241 SF4 FS4 . N 4 SF4 B 1 1242 1242 SF4 FS4 . O 5 TPP B 1 1243 1243 TPP TPP . P 6 PYR B 1 1246 1246 PYR PYR . Q 7 HOH A 1 2001 2001 HOH HOH . Q 7 HOH A 2 2002 2002 HOH HOH . Q 7 HOH A 3 2003 2003 HOH HOH . Q 7 HOH A 4 2004 2004 HOH HOH . Q 7 HOH A 5 2005 2005 HOH HOH . Q 7 HOH A 6 2106 2106 HOH HOH . Q 7 HOH A 7 2107 2107 HOH HOH . R 7 HOH B 1 2006 2006 HOH HOH . R 7 HOH B 2 2007 2007 HOH HOH . R 7 HOH B 3 2101 2101 HOH HOH . R 7 HOH B 4 2102 2102 HOH HOH . R 7 HOH B 5 2103 2103 HOH HOH . R 7 HOH B 6 2104 2104 HOH HOH . R 7 HOH B 7 2105 2105 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' TPP . . . O 5 -17.713 -47.394 32.271 1 16.71 ? N1' TPP 1243 B 1 HETATM 2 C C2' TPP . . . O 5 -19.068 -47.402 32.554 1 16.6 ? C2' TPP 1243 B 1 HETATM 3 C CM2 TPP . . . O 5 -19.897 -48.62 32.317 1 16.44 ? CM2 TPP 1243 B 1 HETATM 4 N N3' TPP . . . O 5 -19.668 -46.348 33.053 1 16.03 ? N3' TPP 1243 B 1 HETATM 5 C C4' TPP . . . O 5 -18.93 -45.196 33.289 1 16.67 ? C4' TPP 1243 B 1 HETATM 6 N N4' TPP . . . O 5 -19.594 -44.171 33.782 1 16.51 ? N4' TPP 1243 B 1 HETATM 7 C C5' TPP . . . O 5 -17.539 -45.157 33.007 1 16.87 ? C5' TPP 1243 B 1 HETATM 8 C C6' TPP . . . O 5 -17 -46.284 32.518 1 16.16 ? C6' TPP 1243 B 1 HETATM 9 C C7' TPP . . . O 5 -16.691 -43.936 33.259 1 16.43 ? C7' TPP 1243 B 1 HETATM 10 N N3 TPP . . . O 5 -17.209 -42.758 32.427 1 16.01 ? N3 TPP 1243 B 1 HETATM 11 C C2 TPP . . . O 5 -18.185 -41.879 32.527 1 16.35 ? C2 TPP 1243 B 1 HETATM 12 S S1 TPP . . . O 5 -17.806 -40.488 31.691 1 15.35 ? S1 TPP 1243 B 1 HETATM 13 C C5 TPP . . . O 5 -16.761 -41.397 30.667 1 15.54 ? C5 TPP 1243 B 1 HETATM 14 C C4 TPP . . . O 5 -16.657 -42.677 31.161 1 15.64 ? C4 TPP 1243 B 1 HETATM 15 C CM4 TPP . . . O 5 -15.836 -43.736 30.551 1 16.15 ? CM4 TPP 1243 B 1 HETATM 16 C C6 TPP . . . O 5 -16.529 -40.888 29.306 1 15.25 ? C6 TPP 1243 B 1 HETATM 17 C C7 TPP . . . O 5 -17.516 -39.871 28.815 1 15.04 ? C7 TPP 1243 B 1 HETATM 18 O O7 TPP . . . O 5 -17.606 -39.888 27.419 1 14.27 ? O7 TPP 1243 B 1 HETATM 19 P PA TPP . . . O 5 -18.093 -38.824 26.367 1 12.99 ? PA TPP 1243 B 1 HETATM 20 O O1A TPP . . . O 5 -19.379 -39.349 25.844 1 13.74 ? O1A TPP 1243 B 1 HETATM 21 O O2A TPP . . . O 5 -17.033 -38.448 25.433 1 13.93 ? O2A TPP 1243 B 1 HETATM 22 O O3A TPP . . . O 5 -18.431 -37.639 27.335 1 13.83 ? O3A TPP 1243 B 1 HETATM 23 P PB TPP . . . O 5 -18.152 -36.054 27.386 1 13.2 ? PB TPP 1243 B 1 HETATM 24 O O1B TPP . . . O 5 -16.974 -35.869 26.451 1 13.94 ? O1B TPP 1243 B 1 HETATM 25 O O2B TPP . . . O 5 -19.357 -35.388 26.732 1 13.45 ? O2B TPP 1243 B 1 HETATM 26 O O3B TPP . . . O 5 -17.773 -35.782 28.762 1 13.51 ? O3B TPP 1243 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 26 #