data_3EY9 # _model_server_result.job_id cfxamUilF7fFRKBeVlL6vQ _model_server_result.datetime_utc '2025-02-16 13:24:22' _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 3ey9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":611}' # _entry.id 3EY9 # _exptl.entry_id 3EY9 _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 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 3EY9 _cell.length_a 151.37 _cell.length_b 151.37 _cell.length_c 153.74 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 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 C N N ? 2 G 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 433 A ASP 433 1_555 F MG MG . A MG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc2 A OD1 ASN 460 A ASN 460 1_555 F MG MG . A MG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc3 C O1A TPP . A TPP 611 1_555 F MG MG . A MG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc4 C O1B TPP . A TPP 611 1_555 F MG MG . A MG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc5 B OD1 ASP 433 B ASP 433 1_555 I MG MG . B MG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc6 B OD1 ASN 460 B ASN 460 1_555 I MG MG . B MG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc7 G O2A TPP . B TPP 611 1_555 I MG MG . B MG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 G O3B TPP . B TPP 611 1_555 I MG MG . B MG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? # _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 399 n y N1' C6' TPP sing 400 n y C2' CM2 TPP sing 401 n n C2' N3' TPP sing 402 n y CM2 HM21 TPP sing 403 n n CM2 HM22 TPP sing 404 n n CM2 HM23 TPP sing 405 n n N3' C4' TPP doub 406 n y C4' N4' TPP sing 407 n n C4' C5' TPP sing 408 n y N4' HN41 TPP sing 409 n n N4' HN42 TPP sing 410 n n C5' C6' TPP doub 411 n y C5' C7' TPP sing 412 n n C6' H6' TPP sing 413 n n C7' N3 TPP sing 414 n n C7' "H7'1" TPP sing 415 n n C7' "H7'2" TPP sing 416 n n N3 C2 TPP doub 417 n y N3 C4 TPP sing 418 n y C2 S1 TPP sing 419 n y C2 H2 TPP sing 420 n n S1 C5 TPP sing 421 n y C5 C4 TPP doub 422 n y C5 C6 TPP sing 423 n n C4 CM4 TPP sing 424 n n CM4 HM41 TPP sing 425 n n CM4 HM42 TPP sing 426 n n CM4 HM43 TPP sing 427 n n C6 C7 TPP sing 428 n n C6 H61 TPP sing 429 n n C6 H62 TPP sing 430 n n C7 O7 TPP sing 431 n n C7 H71 TPP sing 432 n n C7 H72 TPP sing 433 n n O7 PA TPP sing 434 n n PA O1A TPP doub 435 n n PA O2A TPP sing 436 n n PA O3A TPP sing 437 n n O2A HOA2 TPP sing 438 n n O3A PB TPP sing 439 n n PB O1B TPP doub 440 n n PB O2B TPP sing 441 n n PB O3B TPP sing 442 n n O2B HOB2 TPP sing 443 n n O3B HOB3 TPP sing 444 n n # _atom_sites.entry_id 3EY9 _atom_sites.fract_transf_matrix[1][1] 0.006606 _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] 0.006606 _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] 0.006504 _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 TPP A 1 611 611 TPP TDP . D 3 FAD A 1 612 612 FAD FAD . E 4 SO4 A 1 621 621 SO4 SO4 . F 5 MG A 1 616 616 MG MG2 . G 2 TPP B 1 611 611 TPP TDP . H 3 FAD B 1 612 612 FAD FAD . I 5 MG B 1 617 617 MG MG2 . J 4 SO4 B 1 621 621 SO4 SO4 . # 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 . . . G 2 59.668 30.115 5.12 1 54.33 ? N1' TPP 611 B 1 HETATM 2 C C2' TPP . . . G 2 59.084 29.463 4.083 1 46.07 ? C2' TPP 611 B 1 HETATM 3 C CM2 TPP . . . G 2 57.961 28.508 4.368 1 34.47 ? CM2 TPP 611 B 1 HETATM 4 N N3' TPP . . . G 2 59.491 29.668 2.804 1 57.14 ? N3' TPP 611 B 1 HETATM 5 C C4' TPP . . . G 2 60.506 30.534 2.557 1 66.55 ? C4' TPP 611 B 1 HETATM 6 N N4' TPP . . . G 2 60.912 30.739 1.28 1 69.27 ? N4' TPP 611 B 1 HETATM 7 C C5' TPP . . . G 2 61.12 31.202 3.615 1 64.5 ? C5' TPP 611 B 1 HETATM 8 C C6' TPP . . . G 2 60.676 30.966 4.913 1 55.13 ? C6' TPP 611 B 1 HETATM 9 C C7' TPP . . . G 2 62.278 32.161 3.396 1 74.97 ? C7' TPP 611 B 1 HETATM 10 N N3 TPP . . . G 2 63.468 31.323 3.179 1 64.97 ? N3 TPP 611 B 1 HETATM 11 C C2 TPP . . . G 2 63.975 31.064 1.949 1 52.08 ? C2 TPP 611 B 1 HETATM 12 S S1 TPP . . . G 2 65.378 30.021 1.905 1 69.5 ? S1 TPP 611 B 1 HETATM 13 C C5 TPP . . . G 2 65.269 29.934 3.626 1 57.6 ? C5 TPP 611 B 1 HETATM 14 C C4 TPP . . . G 2 64.146 30.72 4.173 1 49.3 ? C4 TPP 611 B 1 HETATM 15 C CM4 TPP . . . G 2 63.849 30.809 5.641 1 41.93 ? CM4 TPP 611 B 1 HETATM 16 C C6 TPP . . . G 2 66.323 29.081 4.278 1 59.33 ? C6 TPP 611 B 1 HETATM 17 C C7 TPP . . . G 2 66.196 27.647 3.777 1 60.96 ? C7 TPP 611 B 1 HETATM 18 O O7 TPP . . . G 2 67.074 26.859 4.579 1 65.28 ? O7 TPP 611 B 1 HETATM 19 P PA TPP . . . G 2 67.637 25.42 4.124 1 65.48 ? PA TPP 611 B 1 HETATM 20 O O1A TPP . . . G 2 66.435 24.544 3.854 1 65.65 ? O1A TPP 611 B 1 HETATM 21 O O2A TPP . . . G 2 68.659 25.041 5.166 1 77.12 ? O2A TPP 611 B 1 HETATM 22 O O3A TPP . . . G 2 68.43 25.703 2.743 1 122.68 ? O3A TPP 611 B 1 HETATM 23 P PB TPP . . . G 2 69.96 26.227 2.687 1 72.7 ? PB TPP 611 B 1 HETATM 24 O O1B TPP . . . G 2 70.606 25.137 1.885 1 66.64 ? O1B TPP 611 B 1 HETATM 25 O O2B TPP . . . G 2 69.906 27.55 1.967 1 72.8 ? O2B TPP 611 B 1 HETATM 26 O O3B TPP . . . G 2 70.403 26.331 4.131 1 55.99 ? O3B TPP 611 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #