data_1PYD # _model_server_result.job_id 3we5MPRTgNiCqR-ZIRdRqw _model_server_result.datetime_utc '2025-03-03 08:39:50' _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 1pyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":557}' # _entry.id 1PYD # _exptl.entry_id 1PYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 3 _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 116.39 _cell.angle_gamma 90 _cell.entry_id 1PYD _cell.length_a 141.95 _cell.length_b 74.67 _cell.length_c 119.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 _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 F 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 metalc ? metalc1 A OD1 ASP 444 A ASP 444 1_555 C MG MG . A MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A OD1 ASN 471 A ASN 471 1_555 C MG MG . A MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc3 A O GLY 473 A GLY 473 1_555 C MG MG . A MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 D O2A TPP . A TPP 557 1_555 C MG MG . A MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc5 D O3B TPP . A TPP 557 1_555 C MG MG . A MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc6 C MG MG . A MG 559 1_555 G O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc7 B OD1 ASP 444 B ASP 444 1_555 E MG MG . B MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc8 B OD1 ASN 471 B ASN 471 1_555 E MG MG . B MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc9 B O GLY 473 B GLY 473 1_555 E MG MG . B MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc10 F O3B TPP . B TPP 557 1_555 E MG MG . B MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc11 F O2A TPP . B TPP 557 1_555 E MG MG . B MG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc12 E MG MG . B MG 559 1_555 H O HOH . B HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 306 n y N1' C6' TPP sing 307 n y C2' CM2 TPP sing 308 n n C2' N3' TPP sing 309 n y CM2 HM21 TPP sing 310 n n CM2 HM22 TPP sing 311 n n CM2 HM23 TPP sing 312 n n N3' C4' TPP doub 313 n y C4' N4' TPP sing 314 n n C4' C5' TPP sing 315 n y N4' HN41 TPP sing 316 n n N4' HN42 TPP sing 317 n n C5' C6' TPP doub 318 n y C5' C7' TPP sing 319 n n C6' H6' TPP sing 320 n n C7' N3 TPP sing 321 n n C7' "H7'1" TPP sing 322 n n C7' "H7'2" TPP sing 323 n n N3 C2 TPP doub 324 n y N3 C4 TPP sing 325 n y C2 S1 TPP sing 326 n y C2 H2 TPP sing 327 n n S1 C5 TPP sing 328 n y C5 C4 TPP doub 329 n y C5 C6 TPP sing 330 n n C4 CM4 TPP sing 331 n n CM4 HM41 TPP sing 332 n n CM4 HM42 TPP sing 333 n n CM4 HM43 TPP sing 334 n n C6 C7 TPP sing 335 n n C6 H61 TPP sing 336 n n C6 H62 TPP sing 337 n n C7 O7 TPP sing 338 n n C7 H71 TPP sing 339 n n C7 H72 TPP sing 340 n n O7 PA TPP sing 341 n n PA O1A TPP doub 342 n n PA O2A TPP sing 343 n n PA O3A TPP sing 344 n n O2A HOA2 TPP sing 345 n n O3A PB TPP sing 346 n n PB O1B TPP doub 347 n n PB O2B TPP sing 348 n n PB O3B TPP sing 349 n n O2B HOB2 TPP sing 350 n n O3B HOB3 TPP sing 351 n n # _atom_sites.entry_id 1PYD _atom_sites.fract_transf_matrix[1][1] 0.007045 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003496 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013392 _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] 0.009307 _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 1 559 559 MG MG . D 3 TPP A 1 557 557 TPP TDP . E 2 MG B 1 559 559 MG MG . F 3 TPP B 1 557 557 TPP TDP . G 4 HOH A 1 560 558 HOH HOH . H 4 HOH B 1 560 558 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 . . . D 3 1.321 10.931 28.151 1 7.15 ? N1' TPP 557 A 1 HETATM 2 C C2' TPP . . . D 3 2.033 9.765 28.239 1 7.16 ? C2' TPP 557 A 1 HETATM 3 C CM2 TPP . . . D 3 1.339 8.437 28.16 1 2.07 ? CM2 TPP 557 A 1 HETATM 4 N N3' TPP . . . D 3 3.341 9.762 28.391 1 6.97 ? N3' TPP 557 A 1 HETATM 5 C C4' TPP . . . D 3 4.012 10.954 28.539 1 6.64 ? C4' TPP 557 A 1 HETATM 6 N N4' TPP . . . D 3 5.325 10.875 28.688 1 6.09 ? N4' TPP 557 A 1 HETATM 7 C C5' TPP . . . D 3 3.31 12.181 28.46 1 6.89 ? C5' TPP 557 A 1 HETATM 8 C C6' TPP . . . D 3 1.985 12.101 28.259 1 7.3 ? C6' TPP 557 A 1 HETATM 9 C C7' TPP . . . D 3 4.006 13.509 28.64 1 7.72 ? C7' TPP 557 A 1 HETATM 10 N N3 TPP . . . D 3 4.591 13.63 30.046 1 5.98 ? N3 TPP 557 A 1 HETATM 11 C C2 TPP . . . D 3 5.888 13.44 30.217 1 5.65 ? C2 TPP 557 A 1 HETATM 12 S S1 TPP . . . D 3 6.428 13.578 31.79 1 4.15 ? S1 TPP 557 A 1 HETATM 13 C C5 TPP . . . D 3 4.839 13.99 32.314 1 6.47 ? C5 TPP 557 A 1 HETATM 14 C C4 TPP . . . D 3 3.96 13.974 31.235 1 5.51 ? C4 TPP 557 A 1 HETATM 15 C CM4 TPP . . . D 3 2.517 14.278 31.326 1 4.74 ? CM4 TPP 557 A 1 HETATM 16 C C6 TPP . . . D 3 4.6 14.297 33.755 1 6.33 ? C6 TPP 557 A 1 HETATM 17 C C7 TPP . . . D 3 4.847 13.199 34.772 1 6.75 ? C7 TPP 557 A 1 HETATM 18 O O7 TPP . . . D 3 4.895 13.732 36.083 1 8.16 ? O7 TPP 557 A 1 HETATM 19 P PA TPP . . . D 3 5.181 13.133 37.527 1 5.24 ? PA TPP 557 A 1 HETATM 20 O O1A TPP . . . D 3 5.035 11.656 37.38 1 9.86 ? O1A TPP 557 A 1 HETATM 21 O O2A TPP . . . D 3 4.434 13.81 38.58 1 5.82 ? O2A TPP 557 A 1 HETATM 22 O O3A TPP . . . D 3 6.717 13.429 37.665 1 8.19 ? O3A TPP 557 A 1 HETATM 23 P PB TPP . . . D 3 7.6 14.543 38.432 1 4.72 ? PB TPP 557 A 1 HETATM 24 O O1B TPP . . . D 3 8.299 15.272 37.392 1 6.3 ? O1B TPP 557 A 1 HETATM 25 O O2B TPP . . . D 3 8.331 13.813 39.556 1 5.68 ? O2B TPP 557 A 1 HETATM 26 O O3B TPP . . . D 3 6.533 15.403 39.087 1 5.69 ? O3B TPP 557 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #