data_1AY0 # _model_server_result.job_id brD5tM6ldx-U99X7QPfVLA _model_server_result.datetime_utc '2025-01-23 15:19:06' _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 1ay0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":682}' # _entry.id 1AY0 # _exptl.entry_id 1AY0 _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 90 _cell.angle_gamma 90 _cell.entry_id 1AY0 _cell.length_a 76.1 _cell.length_b 113.6 _cell.length_c 162 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AY0 _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 _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 _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 OD2 ASP 157 A ASP 157 1_555 C CA CA . A CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 A OD1 ASN 187 A ASN 187 1_555 C CA CA . A CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc3 A O ILE 189 A ILE 189 1_555 C CA CA . A CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc4 C CA CA . A CA 681 1_555 D O3B TPP . A TPP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc5 C CA CA . A CA 681 1_555 D O1A TPP . A TPP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc6 B OD2 ASP 157 B ASP 157 1_555 E CA CA . B CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc7 B OD1 ASN 187 B ASN 187 1_555 E CA CA . B CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc8 B O ILE 189 B ILE 189 1_555 E CA CA . B CA 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc9 E CA CA . B CA 681 1_555 F O1A TPP . B TPP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc10 E CA CA . B CA 681 1_555 F O2B TPP . B TPP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? # _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 304 n y N1' C6' TPP sing 305 n y C2' CM2 TPP sing 306 n n C2' N3' TPP sing 307 n y CM2 HM21 TPP sing 308 n n CM2 HM22 TPP sing 309 n n CM2 HM23 TPP sing 310 n n N3' C4' TPP doub 311 n y C4' N4' TPP sing 312 n n C4' C5' TPP sing 313 n y N4' HN41 TPP sing 314 n n N4' HN42 TPP sing 315 n n C5' C6' TPP doub 316 n y C5' C7' TPP sing 317 n n C6' H6' TPP sing 318 n n C7' N3 TPP sing 319 n n C7' "H7'1" TPP sing 320 n n C7' "H7'2" TPP sing 321 n n N3 C2 TPP doub 322 n y N3 C4 TPP sing 323 n y C2 S1 TPP sing 324 n y C2 H2 TPP sing 325 n n S1 C5 TPP sing 326 n y C5 C4 TPP doub 327 n y C5 C6 TPP sing 328 n n C4 CM4 TPP sing 329 n n CM4 HM41 TPP sing 330 n n CM4 HM42 TPP sing 331 n n CM4 HM43 TPP sing 332 n n C6 C7 TPP sing 333 n n C6 H61 TPP sing 334 n n C6 H62 TPP sing 335 n n C7 O7 TPP sing 336 n n C7 H71 TPP sing 337 n n C7 H72 TPP sing 338 n n O7 PA TPP sing 339 n n PA O1A TPP doub 340 n n PA O2A TPP sing 341 n n PA O3A TPP sing 342 n n O2A HOA2 TPP sing 343 n n O3A PB TPP sing 344 n n PB O1B TPP doub 345 n n PB O2B TPP sing 346 n n PB O3B TPP sing 347 n n O2B HOB2 TPP sing 348 n n O3B HOB3 TPP sing 349 n n # _atom_sites.entry_id 1AY0 _atom_sites.fract_transf_matrix[1][1] 0.013141 _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] 0.008803 _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] 0.006173 _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 CA A 1 681 681 CA CA . D 3 TPP A 1 682 682 TPP TPP . E 2 CA B 1 681 681 CA CA . F 3 TPP B 1 682 682 TPP TPP . # 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 -3.016 61.014 19.944 1 14.53 ? N1' TPP 682 A 1 HETATM 2 C C2' TPP . . . D 3 -2.322 60.065 20.574 1 14.17 ? C2' TPP 682 A 1 HETATM 3 C CM2 TPP . . . D 3 -1.04 60.4 21.102 1 15.27 ? CM2 TPP 682 A 1 HETATM 4 N N3' TPP . . . D 3 -2.799 58.863 20.729 1 12.7 ? N3' TPP 682 A 1 HETATM 5 C C4' TPP . . . D 3 -3.975 58.518 20.074 1 16.53 ? C4' TPP 682 A 1 HETATM 6 N N4' TPP . . . D 3 -4.353 57.297 20.183 1 12.85 ? N4' TPP 682 A 1 HETATM 7 C C5' TPP . . . D 3 -4.777 59.493 19.452 1 16.01 ? C5' TPP 682 A 1 HETATM 8 C C6' TPP . . . D 3 -4.239 60.733 19.38 1 15.45 ? C6' TPP 682 A 1 HETATM 9 C C7' TPP . . . D 3 -6.111 59.182 18.893 1 20.92 ? C7' TPP 682 A 1 HETATM 10 N N3 TPP . . . D 3 -5.862 58.433 17.621 1 25.46 ? N3 TPP 682 A 1 HETATM 11 C C2 TPP . . . D 3 -6.172 57.131 17.518 1 26.85 ? C2 TPP 682 A 1 HETATM 12 S S1 TPP . . . D 3 -6.304 56.619 15.923 1 28.22 ? S1 TPP 682 A 1 HETATM 13 C C5 TPP . . . D 3 -5.809 58.163 15.399 1 27.01 ? C5 TPP 682 A 1 HETATM 14 C C4 TPP . . . D 3 -5.739 59.031 16.456 1 25.35 ? C4 TPP 682 A 1 HETATM 15 C CM4 TPP . . . D 3 -5.885 60.471 16.394 1 22.46 ? CM4 TPP 682 A 1 HETATM 16 C C6 TPP . . . D 3 -6.021 58.516 13.957 1 27.2 ? C6 TPP 682 A 1 HETATM 17 C C7 TPP . . . D 3 -5.726 57.461 12.934 1 25.65 ? C7 TPP 682 A 1 HETATM 18 O O7 TPP . . . D 3 -4.306 57.398 12.731 1 28.77 ? O7 TPP 682 A 1 HETATM 19 P PA TPP . . . D 3 -3.731 56.554 11.569 1 26.45 ? PA TPP 682 A 1 HETATM 20 O O1A TPP . . . D 3 -4.044 57.426 10.46 1 22.04 ? O1A TPP 682 A 1 HETATM 21 O O2A TPP . . . D 3 -2.274 56.296 11.873 1 26.62 ? O2A TPP 682 A 1 HETATM 22 O O3A TPP . . . D 3 -4.631 55.242 11.449 1 25.6 ? O3A TPP 682 A 1 HETATM 23 P PB TPP . . . D 3 -5.463 54.369 10.415 1 26.43 ? PB TPP 682 A 1 HETATM 24 O O1B TPP . . . D 3 -5.357 52.954 10.788 1 27.76 ? O1B TPP 682 A 1 HETATM 25 O O2B TPP . . . D 3 -6.821 54.892 10.597 1 26.94 ? O2B TPP 682 A 1 HETATM 26 O O3B TPP . . . D 3 -4.835 54.596 9.103 1 27.7 ? O3B TPP 682 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 26 #