data_5NPU # _model_server_result.job_id hbTIaoAHZ7O26N0WIt1dgw _model_server_result.datetime_utc '2024-10-19 10:22:38' _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 5npu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":602}' # _entry.id 5NPU # _exptl.entry_id 5NPU _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 4 _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 5NPU _cell.length_a 108.33 _cell.length_b 108.33 _cell.length_c 322.651 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NPU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # 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 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 PISA monomeric 1 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,N 1 1 B,G,H 2 1 C,I,J,K 3 1 D,L,M 4 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 F N N ? 3 H N N ? 3 J N N ? 3 M 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 441 A ASP 441 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc2 A OD1 ASN 468 A ASN 468 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc3 E MG MG . A MG 601 1_555 F O1A TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc4 E MG MG . A MG 601 1_555 F O1B TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 E MG MG . A MG 601 1_555 F O2B TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc6 B OD1 ASP 441 B ASP 441 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc7 B OD1 ASN 468 B ASN 468 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc8 B O GLY 470 B GLY 470 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc9 G MG MG . B MG 601 1_555 H O2A TPP . B TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc10 C OD1 ASP 441 C ASP 441 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc11 C OD1 ASN 468 C ASN 468 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc12 C O GLY 470 C GLY 470 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc13 I MG MG . C MG 601 1_555 J O1B TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc14 I MG MG . C MG 601 1_555 J O1A TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc15 D OD1 ASP 441 D ASP 441 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc16 D OD1 ASN 468 D ASN 468 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc17 D O GLY 470 D GLY 470 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc18 L MG MG . D MG 601 1_555 M O2B TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc19 L MG MG . D MG 601 1_555 M O2A TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? # _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 322 n y N1' C6' TPP sing 323 n y C2' CM2 TPP sing 324 n n C2' N3' TPP sing 325 n y CM2 HM21 TPP sing 326 n n CM2 HM22 TPP sing 327 n n CM2 HM23 TPP sing 328 n n N3' C4' TPP doub 329 n y C4' N4' TPP sing 330 n n C4' C5' TPP sing 331 n y N4' HN41 TPP sing 332 n n N4' HN42 TPP sing 333 n n C5' C6' TPP doub 334 n y C5' C7' TPP sing 335 n n C6' H6' TPP sing 336 n n C7' N3 TPP sing 337 n n C7' "H7'1" TPP sing 338 n n C7' "H7'2" TPP sing 339 n n N3 C2 TPP doub 340 n y N3 C4 TPP sing 341 n y C2 S1 TPP sing 342 n y C2 H2 TPP sing 343 n n S1 C5 TPP sing 344 n y C5 C4 TPP doub 345 n y C5 C6 TPP sing 346 n n C4 CM4 TPP sing 347 n n CM4 HM41 TPP sing 348 n n CM4 HM42 TPP sing 349 n n CM4 HM43 TPP sing 350 n n C6 C7 TPP sing 351 n n C6 H61 TPP sing 352 n n C6 H62 TPP sing 353 n n C7 O7 TPP sing 354 n n C7 H71 TPP sing 355 n n C7 H72 TPP sing 356 n n O7 PA TPP sing 357 n n PA O1A TPP doub 358 n n PA O2A TPP sing 359 n n PA O3A TPP sing 360 n n O2A HOA2 TPP sing 361 n n O3A PB TPP sing 362 n n PB O1B TPP doub 363 n n PB O2B TPP sing 364 n n PB O3B TPP sing 365 n n O2B HOB2 TPP sing 366 n n O3B HOB3 TPP sing 367 n n # _atom_sites.entry_id 5NPU _atom_sites.fract_transf_matrix[1][1] 0.009231 _atom_sites.fract_transf_matrix[1][2] 0.00533 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010659 _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] 0.003099 _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 E 2 MG A 1 601 601 MG MG . F 3 TPP A 1 602 602 TPP TPP . G 2 MG B 1 601 601 MG MG . H 3 TPP B 1 602 602 TPP TPP . I 2 MG C 1 601 601 MG MG . J 3 TPP C 1 602 602 TPP TPP . K 4 PEG C 1 603 1 PEG PEG . L 2 MG D 1 601 601 MG MG . M 3 TPP D 1 602 602 TPP TPP . N 5 HOH A 1 701 1 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 . . . M 3 -28 -68.846 -2.596 1 67.5 ? N1' TPP 602 D 1 HETATM 2 C C2' TPP . . . M 3 -28.572 -68.083 -3.594 1 67.65 ? C2' TPP 602 D 1 HETATM 3 C CM2 TPP . . . M 3 -29.857 -67.342 -3.355 1 72.95 ? CM2 TPP 602 D 1 HETATM 4 N N3' TPP . . . M 3 -27.948 -67.978 -4.817 1 67.69 ? N3' TPP 602 D 1 HETATM 5 C C4' TPP . . . M 3 -26.771 -68.65 -5.069 1 68.07 ? C4' TPP 602 D 1 HETATM 6 N N4' TPP . . . M 3 -26.215 -68.522 -6.271 1 67.96 ? N4' TPP 602 D 1 HETATM 7 C C5' TPP . . . M 3 -26.186 -69.427 -4.07 1 69.79 ? C5' TPP 602 D 1 HETATM 8 C C6' TPP . . . M 3 -26.817 -69.52 -2.829 1 67.97 ? C6' TPP 602 D 1 HETATM 9 C C7' TPP . . . M 3 -24.894 -70.18 -4.326 1 69.81 ? C7' TPP 602 D 1 HETATM 10 N N3 TPP . . . M 3 -25.153 -71.334 -5.161 1 81.06 ? N3 TPP 602 D 1 HETATM 11 C C2 TPP . . . M 3 -24.924 -71.354 -6.517 1 89.76 ? C2 TPP 602 D 1 HETATM 12 S S1 TPP . . . M 3 -25.307 -72.745 -7.21 1 107.29 ? S1 TPP 602 D 1 HETATM 13 C C5 TPP . . . M 3 -25.739 -73.415 -5.83 1 112.83 ? C5 TPP 602 D 1 HETATM 14 C C4 TPP . . . M 3 -25.622 -72.545 -4.739 1 103.42 ? C4 TPP 602 D 1 HETATM 15 C CM4 TPP . . . M 3 -25.978 -72.925 -3.324 1 110.65 ? CM4 TPP 602 D 1 HETATM 16 C C6 TPP . . . M 3 -26.214 -74.854 -5.917 1 122.5 ? C6 TPP 602 D 1 HETATM 17 C C7 TPP . . . M 3 -27.418 -75.127 -6.836 1 122.45 ? C7 TPP 602 D 1 HETATM 18 O O7 TPP . . . M 3 -27.875 -76.468 -6.624 1 112 ? O7 TPP 602 D 1 HETATM 19 P PA TPP . . . M 3 -28.966 -77.331 -7.471 1 84.37 ? PA TPP 602 D 1 HETATM 20 O O1A TPP . . . M 3 -30.329 -76.671 -7.497 1 81.52 ? O1A TPP 602 D 1 HETATM 21 O O2A TPP . . . M 3 -29.14 -78.692 -6.839 1 82.57 ? O2A TPP 602 D 1 HETATM 22 O O3A TPP . . . M 3 -28.436 -77.482 -8.985 1 82.22 ? O3A TPP 602 D 1 HETATM 23 P PB TPP . . . M 3 -27.819 -78.839 -9.575 1 83.6 ? PB TPP 602 D 1 HETATM 24 O O1B TPP . . . M 3 -27.692 -78.747 -11.074 1 84.46 ? O1B TPP 602 D 1 HETATM 25 O O2B TPP . . . M 3 -28.765 -79.958 -9.184 1 85.32 ? O2B TPP 602 D 1 HETATM 26 O O3B TPP . . . M 3 -26.487 -79.084 -8.923 1 82.21 ? O3B TPP 602 D 1 HETATM 27 H HM21 TPP . . . M 3 -30.608 -67.677 -4.07 1 87.54 ? HM21 TPP 602 D 1 HETATM 28 H HM22 TPP . . . M 3 -29.688 -66.272 -3.48 1 87.54 ? HM22 TPP 602 D 1 HETATM 29 H HM23 TPP . . . M 3 -30.206 -67.539 -2.342 1 87.54 ? HM23 TPP 602 D 1 HETATM 30 H HN41 TPP . . . M 3 -25.342 -68.998 -6.479 1 81.55 ? HN41 TPP 602 D 1 HETATM 31 H HN42 TPP . . . M 3 -26.664 -67.953 -6.98 1 81.55 ? HN42 TPP 602 D 1 HETATM 32 H H6' TPP . . . M 3 -26.373 -70.127 -2.039 1 81.57 ? H6' TPP 602 D 1 HETATM 33 H "H7'1" TPP . . . M 3 -24.463 -70.502 -3.378 1 83.77 ? "H7'1" TPP 602 D 1 HETATM 34 H "H7'2" TPP . . . M 3 -24.177 -69.524 -4.819 1 83.77 ? "H7'2" TPP 602 D 1 HETATM 35 H H2 TPP . . . M 3 -24.045 -70.956 -7.025 1 107.71 ? H2 TPP 602 D 1 HETATM 36 H HM41 TPP . . . M 3 -25.363 -73.767 -3.008 1 132.78 ? HM41 TPP 602 D 1 HETATM 37 H HM42 TPP . . . M 3 -27.03 -73.205 -3.277 1 132.78 ? HM42 TPP 602 D 1 HETATM 38 H HM43 TPP . . . M 3 -25.798 -72.076 -2.664 1 132.78 ? HM43 TPP 602 D 1 HETATM 39 H H61 TPP . . . M 3 -26.468 -75.191 -4.912 1 147 ? H61 TPP 602 D 1 HETATM 40 H H62 TPP . . . M 3 -25.38 -75.469 -6.255 1 147 ? H62 TPP 602 D 1 HETATM 41 H H71 TPP . . . M 3 -27.127 -74.996 -7.878 1 146.94 ? H71 TPP 602 D 1 HETATM 42 H H72 TPP . . . M 3 -28.221 -74.424 -6.614 1 146.94 ? H72 TPP 602 D 1 # _model_server_stats.io_time_ms 152 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 42 #