data_3EXF # _model_server_result.job_id oTcu1SJoAzMiLsBRrhFZfg _model_server_result.datetime_utc '2025-06-28 13:03:09' _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 3exf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1009}' # _entry.id 3EXF # _exptl.entry_id 3EXF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 4 _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 109.15 _cell.angle_gamma 90 _cell.entry_id 3EXF _cell.length_a 103.389 _cell.length_b 129.668 _cell.length_c 144.946 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,I,J,K,L,M,N,U,V,W 1 1 E,F,G,H,O,P,Q,R,S,T,X,Y,Z 2 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 ? 4 J N N ? 4 M N N ? 4 P N N ? 4 S 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 188 A ASP 167 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc2 A OD1 ASN 217 A ASN 196 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc3 A O TYR 219 A TYR 198 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc4 I MG MG . A MG 1001 1_555 J O1B TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc5 I MG MG . A MG 1001 1_555 J O2A TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc6 B O ALA 160 B ALA 160 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc7 B O ILE 161 B ILE 161 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc8 B O ASP 163 B ASP 163 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc9 C OD2 ASP 188 C ASP 167 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc10 C OD1 ASN 217 C ASN 196 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc11 C O TYR 219 C TYR 198 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc12 L MG MG . C MG 1004 1_555 M O1B TPP . C TPP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc13 L MG MG . C MG 1004 1_555 M O2A TPP . C TPP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc14 L MG MG . C MG 1004 1_555 V O HOH . C HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc15 D O ILE 161 D ILE 161 1_555 N K K . D K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc16 E OD2 ASP 188 E ASP 167 1_555 O MG MG . E MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc17 E O TYR 219 E TYR 198 1_555 O MG MG . E MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc18 O MG MG . E MG 1007 1_555 P O2A TPP . E TPP 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc19 O MG MG . E MG 1007 1_555 P O1B TPP . E TPP 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? metalc ? metalc20 F O ILE 161 F ILE 161 1_555 Q K K . F K 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc21 F O ASP 163 F ASP 163 1_555 Q K K . F K 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc22 G OD2 ASP 188 G ASP 167 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.883 ? metalc ? metalc23 G OD1 ASN 217 G ASN 196 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc24 G O TYR 219 G TYR 198 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc25 R MG MG . G MG 1010 1_555 S O2A TPP . G TPP 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc26 R MG MG . G MG 1010 1_555 S O1B TPP . G TPP 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc27 H O ASP 163 H ASP 163 1_555 T K K . H K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? # _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 3EXF _atom_sites.fract_transf_matrix[1][1] 0.009672 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003359 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007712 _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] 0.007303 _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 I 3 MG A 1 1001 1001 MG MG . J 4 TPP A 1 1003 1003 TPP TPP . K 5 K B 1 1005 1005 K K . L 3 MG C 1 1004 1004 MG MG . M 4 TPP C 1 1006 1006 TPP TPP . N 5 K D 1 1002 1002 K K . O 3 MG E 1 1007 1007 MG MG . P 4 TPP E 1 1009 1009 TPP TPP . Q 5 K F 1 1011 1011 K K . R 3 MG G 1 1010 1010 MG MG . S 4 TPP G 1 1012 1012 TPP TPP . T 5 K H 1 1008 1008 K K . U 6 HOH B 1 2004 2004 HOH HOH . V 6 HOH C 1 2002 2002 HOH HOH . V 6 HOH C 2 2006 2006 HOH HOH . V 6 HOH C 3 2009 2009 HOH HOH . W 6 HOH D 1 2001 2001 HOH HOH . X 6 HOH E 1 2007 2007 HOH HOH . Y 6 HOH F 1 2005 2005 HOH HOH . Y 6 HOH F 2 2008 2008 HOH HOH . Z 6 HOH H 1 2003 2003 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 . . . P 4 -56.815 -30.942 -60.907 1 27.1 ? N1' TPP 1009 E 1 HETATM 2 C C2' TPP . . . P 4 -56.639 -31.467 -62.172 1 27.91 ? C2' TPP 1009 E 1 HETATM 3 C CM2 TPP . . . P 4 -55.606 -32.533 -62.41 1 27.55 ? CM2 TPP 1009 E 1 HETATM 4 N N3' TPP . . . P 4 -57.443 -31.03 -63.215 1 27.33 ? N3' TPP 1009 E 1 HETATM 5 C C4' TPP . . . P 4 -58.402 -30.069 -62.976 1 26.21 ? C4' TPP 1009 E 1 HETATM 6 N N4' TPP . . . P 4 -59.128 -29.664 -63.999 1 24.18 ? N4' TPP 1009 E 1 HETATM 7 C C5' TPP . . . P 4 -58.576 -29.544 -61.698 1 27.14 ? C5' TPP 1009 E 1 HETATM 8 C C6' TPP . . . P 4 -57.779 -29.985 -60.659 1 26.96 ? C6' TPP 1009 E 1 HETATM 9 C C7' TPP . . . P 4 -59.574 -28.465 -61.41 1 30.72 ? C7' TPP 1009 E 1 HETATM 10 N N3 TPP . . . P 4 -58.977 -27.197 -61.795 1 36.08 ? N3 TPP 1009 E 1 HETATM 11 C C2 TPP . . . P 4 -59.225 -26.662 -63.042 1 37.39 ? C2 TPP 1009 E 1 HETATM 12 S S1 TPP . . . P 4 -58.476 -25.258 -63.283 1 40.35 ? S1 TPP 1009 E 1 HETATM 13 C C5 TPP . . . P 4 -57.801 -25.219 -61.82 1 37.55 ? C5 TPP 1009 E 1 HETATM 14 C C4 TPP . . . P 4 -58.137 -26.348 -61.058 1 38.12 ? C4 TPP 1009 E 1 HETATM 15 C CM4 TPP . . . P 4 -57.611 -26.516 -59.653 1 37.85 ? CM4 TPP 1009 E 1 HETATM 16 C C6 TPP . . . P 4 -56.938 -24.002 -61.512 1 33.85 ? C6 TPP 1009 E 1 HETATM 17 C C7 TPP . . . P 4 -55.802 -23.813 -62.543 1 29.47 ? C7 TPP 1009 E 1 HETATM 18 O O7 TPP . . . P 4 -55.451 -22.469 -62.855 1 24.57 ? O7 TPP 1009 E 1 HETATM 19 P PA TPP . . . P 4 -54.048 -22.187 -63.583 1 22.62 ? PA TPP 1009 E 1 HETATM 20 O O1A TPP . . . P 4 -53.075 -23.316 -63.518 1 21.64 ? O1A TPP 1009 E 1 HETATM 21 O O2A TPP . . . P 4 -53.385 -20.917 -63.134 1 26.99 ? O2A TPP 1009 E 1 HETATM 22 O O3A TPP . . . P 4 -54.539 -21.868 -65.067 1 23.37 ? O3A TPP 1009 E 1 HETATM 23 P PB TPP . . . P 4 -55.446 -20.538 -65.279 1 18.73 ? PB TPP 1009 E 1 HETATM 24 O O1B TPP . . . P 4 -55.228 -19.57 -64.167 1 18.87 ? O1B TPP 1009 E 1 HETATM 25 O O2B TPP . . . P 4 -55.087 -19.826 -66.563 1 19.25 ? O2B TPP 1009 E 1 HETATM 26 O O3B TPP . . . P 4 -56.893 -20.957 -65.409 1 18.57 ? O3B TPP 1009 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #