data_8X3Z # _model_server_result.job_id IBoqOQpUDtZU_m4me17ccw _model_server_result.datetime_utc '2024-11-21 09:32:14' _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 8x3z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 8X3Z # _exptl.entry_id 8X3Z _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 1 _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 8X3Z _cell.length_a 58.916 _cell.length_b 129.734 _cell.length_c 220.675 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X3Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,G,H _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B OD1 ASP 430 B ASP 430 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc2 B OD2 ASP 430 B ASP 430 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc3 B OD1 ASN 457 B ASN 457 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 B O ARG 459 B ARG 459 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 D O1A TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc6 D O1B TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc7 D O3B TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 350 n y N1' C6' TPP sing 351 n y C2' CM2 TPP sing 352 n n C2' N3' TPP sing 353 n y CM2 HM21 TPP sing 354 n n CM2 HM22 TPP sing 355 n n CM2 HM23 TPP sing 356 n n N3' C4' TPP doub 357 n y C4' N4' TPP sing 358 n n C4' C5' TPP sing 359 n y N4' HN41 TPP sing 360 n n N4' HN42 TPP sing 361 n n C5' C6' TPP doub 362 n y C5' C7' TPP sing 363 n n C6' H6' TPP sing 364 n n C7' N3 TPP sing 365 n n C7' "H7'1" TPP sing 366 n n C7' "H7'2" TPP sing 367 n n N3 C2 TPP doub 368 n y N3 C4 TPP sing 369 n y C2 S1 TPP sing 370 n y C2 H2 TPP sing 371 n n S1 C5 TPP sing 372 n y C5 C4 TPP doub 373 n y C5 C6 TPP sing 374 n n C4 CM4 TPP sing 375 n n CM4 HM41 TPP sing 376 n n CM4 HM42 TPP sing 377 n n CM4 HM43 TPP sing 378 n n C6 C7 TPP sing 379 n n C6 H61 TPP sing 380 n n C6 H62 TPP sing 381 n n C7 O7 TPP sing 382 n n C7 H71 TPP sing 383 n n C7 H72 TPP sing 384 n n O7 PA TPP sing 385 n n PA O1A TPP doub 386 n n PA O2A TPP sing 387 n n PA O3A TPP sing 388 n n O2A HOA2 TPP sing 389 n n O3A PB TPP sing 390 n n PB O1B TPP doub 391 n n PB O2B TPP sing 392 n n PB O3B TPP sing 393 n n O2B HOB2 TPP sing 394 n n O3B HOB3 TPP sing 395 n n # _atom_sites.entry_id 8X3Z _atom_sites.fract_transf_matrix[1][1] 0.016973 _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] 0.007708 _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] 0.004532 _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 ADP A 1 601 601 ADP ADP . D 3 TPP B 1 601 601 TPP TPP . E 2 ADP B 1 602 701 ADP ADP . F 4 MG B 1 603 801 MG MG . G 5 HOH A 1 701 51 HOH HOH . G 5 HOH A 2 702 79 HOH HOH . G 5 HOH A 3 703 119 HOH HOH . G 5 HOH A 4 704 50 HOH HOH . G 5 HOH A 5 705 86 HOH HOH . G 5 HOH A 6 706 7 HOH HOH . G 5 HOH A 7 707 27 HOH HOH . G 5 HOH A 8 708 32 HOH HOH . G 5 HOH A 9 709 49 HOH HOH . G 5 HOH A 10 710 8 HOH HOH . G 5 HOH A 11 711 15 HOH HOH . G 5 HOH A 12 712 29 HOH HOH . G 5 HOH A 13 713 75 HOH HOH . G 5 HOH A 14 714 106 HOH HOH . G 5 HOH A 15 715 111 HOH HOH . G 5 HOH A 16 716 11 HOH HOH . G 5 HOH A 17 717 57 HOH HOH . G 5 HOH A 18 718 1 HOH HOH . G 5 HOH A 19 719 96 HOH HOH . G 5 HOH A 20 720 23 HOH HOH . G 5 HOH A 21 721 82 HOH HOH . G 5 HOH A 22 722 62 HOH HOH . G 5 HOH A 23 723 85 HOH HOH . G 5 HOH A 24 724 73 HOH HOH . G 5 HOH A 25 725 26 HOH HOH . G 5 HOH A 26 726 43 HOH HOH . G 5 HOH A 27 727 53 HOH HOH . G 5 HOH A 28 728 66 HOH HOH . G 5 HOH A 29 729 38 HOH HOH . G 5 HOH A 30 730 90 HOH HOH . G 5 HOH A 31 731 77 HOH HOH . G 5 HOH A 32 732 84 HOH HOH . G 5 HOH A 33 733 125 HOH HOH . G 5 HOH A 34 734 116 HOH HOH . G 5 HOH A 35 735 122 HOH HOH . H 5 HOH B 1 701 104 HOH HOH . H 5 HOH B 2 702 59 HOH HOH . H 5 HOH B 3 703 14 HOH HOH . H 5 HOH B 4 704 92 HOH HOH . H 5 HOH B 5 705 46 HOH HOH . H 5 HOH B 6 706 31 HOH HOH . H 5 HOH B 7 707 4 HOH HOH . H 5 HOH B 8 708 118 HOH HOH . H 5 HOH B 9 709 10 HOH HOH . H 5 HOH B 10 710 121 HOH HOH . H 5 HOH B 11 711 3 HOH HOH . H 5 HOH B 12 712 61 HOH HOH . H 5 HOH B 13 713 54 HOH HOH . H 5 HOH B 14 714 20 HOH HOH . H 5 HOH B 15 715 21 HOH HOH . H 5 HOH B 16 716 72 HOH HOH . H 5 HOH B 17 717 24 HOH HOH . H 5 HOH B 18 718 105 HOH HOH . H 5 HOH B 19 719 6 HOH HOH . H 5 HOH B 20 720 76 HOH HOH . H 5 HOH B 21 721 13 HOH HOH . H 5 HOH B 22 722 16 HOH HOH . H 5 HOH B 23 723 17 HOH HOH . H 5 HOH B 24 724 63 HOH HOH . H 5 HOH B 25 725 34 HOH HOH . H 5 HOH B 26 726 42 HOH HOH . H 5 HOH B 27 727 37 HOH HOH . H 5 HOH B 28 728 28 HOH HOH . H 5 HOH B 29 729 47 HOH HOH . H 5 HOH B 30 730 65 HOH HOH . H 5 HOH B 31 731 56 HOH HOH . H 5 HOH B 32 732 88 HOH HOH . H 5 HOH B 33 733 18 HOH HOH . H 5 HOH B 34 734 112 HOH HOH . H 5 HOH B 35 735 36 HOH HOH . H 5 HOH B 36 736 40 HOH HOH . H 5 HOH B 37 737 22 HOH HOH . H 5 HOH B 38 738 109 HOH HOH . H 5 HOH B 39 739 80 HOH HOH . H 5 HOH B 40 740 117 HOH HOH . H 5 HOH B 41 741 113 HOH HOH . H 5 HOH B 42 742 93 HOH HOH . H 5 HOH B 43 743 89 HOH HOH . H 5 HOH B 44 744 64 HOH HOH . H 5 HOH B 45 745 94 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 . . . D 3 -9.444 -24.595 30.537 1 36.35 ? N1' TPP 601 B 1 HETATM 2 C C2' TPP . . . D 3 -10.159 -23.501 30.476 1 39.45 ? C2' TPP 601 B 1 HETATM 3 C CM2 TPP . . . D 3 -11.587 -23.524 30.718 1 42.91 ? CM2 TPP 601 B 1 HETATM 4 N N3' TPP . . . D 3 -9.654 -22.345 30.201 1 45.02 ? N3' TPP 601 B 1 HETATM 5 C C4' TPP . . . D 3 -8.371 -22.244 30.003 1 48.97 ? C4' TPP 601 B 1 HETATM 6 N N4' TPP . . . D 3 -7.874 -21.087 29.727 1 50.56 ? N4' TPP 601 B 1 HETATM 7 C C5' TPP . . . D 3 -7.528 -23.39 30.046 1 52.64 ? C5' TPP 601 B 1 HETATM 8 C C6' TPP . . . D 3 -8.146 -24.571 30.344 1 38.61 ? C6' TPP 601 B 1 HETATM 9 C C7' TPP . . . D 3 -6.053 -23.319 29.787 1 65.47 ? C7' TPP 601 B 1 HETATM 10 N N3 TPP . . . D 3 -5.481 -22.874 28.514 1 77.99 ? N3 TPP 601 B 1 HETATM 11 C C2 TPP . . . D 3 -4.976 -21.665 28.229 1 78.57 ? C2 TPP 601 B 1 HETATM 12 S S1 TPP . . . D 3 -4.374 -21.489 26.612 1 85.07 ? S1 TPP 601 B 1 HETATM 13 C C5 TPP . . . D 3 -4.769 -23.095 26.274 1 83.74 ? C5 TPP 601 B 1 HETATM 14 C C4 TPP . . . D 3 -5.366 -23.714 27.456 1 80.93 ? C4 TPP 601 B 1 HETATM 15 C CM4 TPP . . . D 3 -5.822 -25.125 27.42 1 77.41 ? CM4 TPP 601 B 1 HETATM 16 C C6 TPP . . . D 3 -4.465 -23.586 24.886 1 85.3 ? C6 TPP 601 B 1 HETATM 17 C C7 TPP . . . D 3 -5.221 -22.755 23.849 1 89.54 ? C7 TPP 601 B 1 HETATM 18 O O7 TPP . . . D 3 -5.896 -23.514 22.843 1 87.17 ? O7 TPP 601 B 1 HETATM 19 P PA TPP . . . D 3 -6.089 -23.065 21.354 1 69.91 ? PA TPP 601 B 1 HETATM 20 O O1A TPP . . . D 3 -5.743 -24.135 20.433 1 49.24 -1 O1A TPP 601 B 1 HETATM 21 O O2A TPP . . . D 3 -7.265 -22.302 21.207 1 66.41 ? O2A TPP 601 B 1 HETATM 22 O O3A TPP . . . D 3 -4.842 -22.174 21.265 1 95.09 ? O3A TPP 601 B 1 HETATM 23 P PB TPP . . . D 3 -3.615 -22.601 20.314 1 101.96 ? PB TPP 601 B 1 HETATM 24 O O1B TPP . . . D 3 -3.209 -23.996 20.612 1 105.18 ? O1B TPP 601 B 1 HETATM 25 O O2B TPP . . . D 3 -2.591 -21.601 20.756 1 21.88 -1 O2B TPP 601 B 1 HETATM 26 O O3B TPP . . . D 3 -4.13 -22.299 18.952 1 89.44 ? O3B TPP 601 B 1 HETATM 27 H HM21 TPP . . . D 3 -11.767 -23.584 31.76 1 51.5 ? HM21 TPP 601 B 1 HETATM 28 H HM22 TPP . . . D 3 -12.026 -22.64 30.334 1 51.5 ? HM22 TPP 601 B 1 HETATM 29 H HM23 TPP . . . D 3 -12.012 -24.367 30.238 1 51.5 ? HM23 TPP 601 B 1 HETATM 30 H HN41 TPP . . . D 3 -8.525 -20.365 29.675 1 60.67 ? HN41 TPP 601 B 1 HETATM 31 H HN42 TPP . . . D 3 -6.895 -20.944 29.539 1 60.67 ? HN42 TPP 601 B 1 HETATM 32 H H6' TPP . . . D 3 -7.571 -25.487 30.4 1 46.33 ? H6' TPP 601 B 1 HETATM 33 H "H7'1" TPP . . . D 3 -5.518 -22.895 30.638 1 78.57 ? "H7'1" TPP 601 B 1 HETATM 34 H "H7'2" TPP . . . D 3 -5.862 -24.384 29.738 1 78.57 ? "H7'2" TPP 601 B 1 HETATM 35 H H2 TPP . . . D 3 -4.895 -20.762 28.822 1 94.28 ? H2 TPP 601 B 1 HETATM 36 H HM41 TPP . . . D 3 -6.792 -25.174 27 1 92.89 ? HM41 TPP 601 B 1 HETATM 37 H HM42 TPP . . . D 3 -5.152 -25.697 26.831 1 92.89 ? HM42 TPP 601 B 1 HETATM 38 H HM43 TPP . . . D 3 -5.843 -25.513 28.405 1 92.89 ? HM43 TPP 601 B 1 HETATM 39 H H61 TPP . . . D 3 -3.392 -23.517 24.698 1 102.36 ? H61 TPP 601 B 1 HETATM 40 H H62 TPP . . . D 3 -4.757 -24.635 24.797 1 102.36 ? H62 TPP 601 B 1 HETATM 41 H H71 TPP . . . D 3 -5.954 -22.133 24.367 1 107.45 ? H71 TPP 601 B 1 HETATM 42 H H72 TPP . . . D 3 -4.515 -22.08 23.361 1 107.45 ? H72 TPP 601 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #