data_3IHK # _model_server_result.job_id zT8QPVIigKiMA4Iq4bZ7xA _model_server_result.datetime_utc '2024-11-14 07:47:56' _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 3ihk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":219}' # _entry.id 3IHK # _exptl.entry_id 3IHK _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 3 _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 3IHK _cell.length_a 105.157 _cell.length_b 105.157 _cell.length_c 121.383 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IHK _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,J,K,L,CA 1 1,2 B,C,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 U N N ? 2 V 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 covale ? covale1 A C VAL 65 A VAL 65 1_555 A N MSE 66 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 66 A MSE 66 1_555 A N ALA 67 A ALA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C HIS 104 A HIS 104 1_555 A N MSE 105 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 105 A MSE 105 1_555 A N LEU 106 A LEU 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 A C PHE 120 A PHE 120 1_555 A N MSE 121 A MSE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C MSE 121 A MSE 121 1_555 A N ARG 122 A ARG 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale7 A C ASP 148 A ASP 148 1_555 A N MSE 149 A MSE 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 A C MSE 149 A MSE 149 1_555 A N VAL 150 A VAL 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 A C PHE 154 A PHE 154 1_555 A N MSE 155 A MSE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale10 A C MSE 155 A MSE 155 1_555 A N ALA 156 A ALA 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 B C VAL 65 B VAL 65 1_555 B N MSE 66 B MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale12 B C MSE 66 B MSE 66 1_555 B N ALA 67 B ALA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale13 B C HIS 104 B HIS 104 1_555 B N MSE 105 B MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C MSE 105 B MSE 105 1_555 B N LEU 106 B LEU 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale15 B C PHE 120 B PHE 120 1_555 B N MSE 121 B MSE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale16 B C MSE 121 B MSE 121 1_555 B N ARG 122 B ARG 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale17 B C ASP 148 B ASP 148 1_555 B N MSE 149 B MSE 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 B C MSE 149 B MSE 149 1_555 B N VAL 150 B VAL 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 B C PHE 154 B PHE 154 1_555 B N MSE 155 B MSE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale20 B C MSE 155 B MSE 155 1_555 B N ALA 156 B ALA 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale21 C C VAL 65 C VAL 65 1_555 C N MSE 66 C MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale22 C C MSE 66 C MSE 66 1_555 C N ALA 67 C ALA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale23 C C HIS 104 C HIS 104 1_555 C N MSE 105 C MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale24 C C MSE 105 C MSE 105 1_555 C N LEU 106 C LEU 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 C C PHE 120 C PHE 120 1_555 C N MSE 121 C MSE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale26 C C MSE 121 C MSE 121 1_555 C N ARG 122 C ARG 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale27 C C ASP 148 C ASP 148 1_555 C N MSE 149 C MSE 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale28 C C MSE 149 C MSE 149 1_555 C N VAL 150 C VAL 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale29 C C PHE 154 C PHE 154 1_555 C N MSE 155 C MSE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale30 C C MSE 155 C MSE 155 1_555 C N ALA 156 C ALA 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A OD2 ASP 47 A ASP 47 1_555 E MG MG . A MG 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc2 A OD2 ASP 75 A ASP 75 1_555 F MG MG . A MG 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc3 E MG MG . A MG 219 1_555 D O3A TPP . A TPP 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc4 B OD1 ASP 47 B ASP 47 1_555 M MG MG . B MG 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc5 B OD2 ASP 75 B ASP 75 1_555 M MG MG . B MG 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? # _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 310 n y N1' C6' TPP sing 311 n y C2' CM2 TPP sing 312 n n C2' N3' TPP sing 313 n y CM2 HM21 TPP sing 314 n n CM2 HM22 TPP sing 315 n n CM2 HM23 TPP sing 316 n n N3' C4' TPP doub 317 n y C4' N4' TPP sing 318 n n C4' C5' TPP sing 319 n y N4' HN41 TPP sing 320 n n N4' HN42 TPP sing 321 n n C5' C6' TPP doub 322 n y C5' C7' TPP sing 323 n n C6' H6' TPP sing 324 n n C7' N3 TPP sing 325 n n C7' "H7'1" TPP sing 326 n n C7' "H7'2" TPP sing 327 n n N3 C2 TPP doub 328 n y N3 C4 TPP sing 329 n y C2 S1 TPP sing 330 n y C2 H2 TPP sing 331 n n S1 C5 TPP sing 332 n y C5 C4 TPP doub 333 n y C5 C6 TPP sing 334 n n C4 CM4 TPP sing 335 n n CM4 HM41 TPP sing 336 n n CM4 HM42 TPP sing 337 n n CM4 HM43 TPP sing 338 n n C6 C7 TPP sing 339 n n C6 H61 TPP sing 340 n n C6 H62 TPP sing 341 n n C7 O7 TPP sing 342 n n C7 H71 TPP sing 343 n n C7 H72 TPP sing 344 n n O7 PA TPP sing 345 n n PA O1A TPP doub 346 n n PA O2A TPP sing 347 n n PA O3A TPP sing 348 n n O2A HOA2 TPP sing 349 n n O3A PB TPP sing 350 n n PB O1B TPP doub 351 n n PB O2B TPP sing 352 n n PB O3B TPP sing 353 n n O2B HOB2 TPP sing 354 n n O3B HOB3 TPP sing 355 n n # _atom_sites.entry_id 3IHK _atom_sites.fract_transf_matrix[1][1] 0.00951 _atom_sites.fract_transf_matrix[1][2] 0.00549 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010981 _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] 0.008238 _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 D 2 TPP A 1 902 902 TPP TPP . E 3 MG A 1 219 219 MG MG . F 3 MG A 1 220 220 MG MG . G 4 PO4 A 1 221 221 PO4 PO4 . H 4 PO4 A 1 222 222 PO4 PO4 . I 4 PO4 A 1 223 223 PO4 PO4 . J 4 PO4 A 1 224 224 PO4 PO4 . K 4 PO4 A 1 225 225 PO4 PO4 . L 4 PO4 A 1 226 226 PO4 PO4 . M 3 MG B 1 219 219 MG MG . N 3 MG B 1 220 220 MG MG . O 4 PO4 B 1 221 221 PO4 PO4 . P 4 PO4 B 1 222 222 PO4 PO4 . Q 4 PO4 B 1 223 223 PO4 PO4 . R 4 PO4 B 1 224 224 PO4 PO4 . S 4 PO4 B 1 225 225 PO4 PO4 . T 4 PO4 B 1 226 226 PO4 PO4 . U 2 TPP C 1 902 902 TPP TPP . V 2 TPP C 1 219 902 TPP TPP . W 3 MG C 1 220 219 MG MG . X 3 MG C 1 221 220 MG MG . Y 4 PO4 C 1 222 221 PO4 PO4 . Z 4 PO4 C 1 223 222 PO4 PO4 . AA 4 PO4 C 1 224 223 PO4 PO4 . BA 4 PO4 C 1 225 224 PO4 PO4 . CA 5 HOH A 1 232 232 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 . . . V 2 10.338 49.299 28.488 1 43.17 ? N1' TPP 219 C 1 HETATM 2 C C2' TPP . . . V 2 10.492 50.192 27.331 1 43.88 ? C2' TPP 219 C 1 HETATM 3 C CM2 TPP . . . V 2 10.69 49.333 26.079 1 42.5 ? CM2 TPP 219 C 1 HETATM 4 N N3' TPP . . . V 2 11.664 51.053 27.531 1 46.2 ? N3' TPP 219 C 1 HETATM 5 C C4' TPP . . . V 2 11.59 51.729 28.679 1 47.81 ? C4' TPP 219 C 1 HETATM 6 N N4' TPP . . . V 2 12.228 52.885 28.811 1 47.22 ? N4' TPP 219 C 1 HETATM 7 C C5' TPP . . . V 2 10.844 51.235 29.736 1 48.42 ? C5' TPP 219 C 1 HETATM 8 C C6' TPP . . . V 2 10.204 50.009 29.604 1 46.27 ? C6' TPP 219 C 1 HETATM 9 C C7' TPP . . . V 2 10.675 51.981 31.063 1 51.04 ? C7' TPP 219 C 1 HETATM 10 N N3 TPP . . . V 2 11.93 51.928 31.823 1 52.04 ? N3 TPP 219 C 1 HETATM 11 C C2 TPP . . . V 2 12.941 50.878 31.582 1 52.91 ? C2 TPP 219 C 1 HETATM 12 S S1 TPP . . . V 2 14.375 51.467 32.545 1 54.22 ? S1 TPP 219 C 1 HETATM 13 C C5 TPP . . . V 2 13.46 52.689 33.39 1 54.54 ? C5 TPP 219 C 1 HETATM 14 C C4 TPP . . . V 2 12.236 52.851 32.733 1 52.8 ? C4 TPP 219 C 1 HETATM 15 C CM4 TPP . . . V 2 11.297 54.017 33.044 1 52.28 ? CM4 TPP 219 C 1 HETATM 16 C C6 TPP . . . V 2 14.01 53.45 34.594 1 59.33 ? C6 TPP 219 C 1 HETATM 17 C C7 TPP . . . V 2 13.807 52.642 35.878 1 65.45 ? C7 TPP 219 C 1 HETATM 18 O O7 TPP . . . V 2 14.44 53.333 36.957 1 73.59 ? O7 TPP 219 C 1 HETATM 19 P PA TPP . . . V 2 14.44 52.712 38.444 1 78.31 ? PA TPP 219 C 1 HETATM 20 O O1A TPP . . . V 2 13.941 51.319 38.39 1 77.75 ? O1A TPP 219 C 1 HETATM 21 O O2A TPP . . . V 2 15.754 52.971 39.074 1 77.52 ? O2A TPP 219 C 1 HETATM 22 O O3A TPP . . . V 2 13.349 53.611 39.216 1 77.75 ? O3A TPP 219 C 1 HETATM 23 P PB TPP . . . V 2 11.78 53.298 39.038 1 78.49 ? PB TPP 219 C 1 HETATM 24 O O1B TPP . . . V 2 11.442 51.865 39.19 1 77.34 ? O1B TPP 219 C 1 HETATM 25 O O2B TPP . . . V 2 11.011 54.219 40.112 1 78.32 ? O2B TPP 219 C 1 HETATM 26 O O3B TPP . . . V 2 11.38 53.859 37.582 1 77.71 ? O3B TPP 219 C 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #