data_1QPB # _model_server_result.job_id 7G30c34vsc1VnsMG7u5Eqw _model_server_result.datetime_utc '2024-11-23 02:08:42' _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 1qpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":600}' # _entry.id 1QPB # _exptl.entry_id 1QPB _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 120.21 _cell.angle_gamma 90 _cell.entry_id 1QPB _cell.length_a 145.049 _cell.length_b 119.7 _cell.length_c 81.283 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QPB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 PQS tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H,I,J 1 1,2 A,B,C,D,E,F,G,H,I,J 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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 145.049 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 F 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 444 A ASP 444 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc2 A OD1 ASN 471 A ASN 471 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc3 A ND2 ASN 471 A ASN 471 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc4 A O GLY 473 A GLY 473 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 C O1A TPP . A TPP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc6 C O3B TPP . A TPP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc7 D MG MG . A MG 601 1_555 I O HOH . A HOH 2077 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc8 B OD1 ASP 444 B ASP 444 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc9 B OD1 ASN 471 B ASN 471 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc10 B O GLY 473 B GLY 473 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc11 F O1A TPP . B TPP 600 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc12 F O3B TPP . B TPP 600 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc13 G MG MG . B MG 601 1_555 J O HOH . B HOH 2043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? # _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 316 n y N1' C6' TPP sing 317 n y C2' CM2 TPP sing 318 n n C2' N3' TPP sing 319 n y CM2 HM21 TPP sing 320 n n CM2 HM22 TPP sing 321 n n CM2 HM23 TPP sing 322 n n N3' C4' TPP doub 323 n y C4' N4' TPP sing 324 n n C4' C5' TPP sing 325 n y N4' HN41 TPP sing 326 n n N4' HN42 TPP sing 327 n n C5' C6' TPP doub 328 n y C5' C7' TPP sing 329 n n C6' H6' TPP sing 330 n n C7' N3 TPP sing 331 n n C7' "H7'1" TPP sing 332 n n C7' "H7'2" TPP sing 333 n n N3 C2 TPP doub 334 n y N3 C4 TPP sing 335 n y C2 S1 TPP sing 336 n y C2 H2 TPP sing 337 n n S1 C5 TPP sing 338 n y C5 C4 TPP doub 339 n y C5 C6 TPP sing 340 n n C4 CM4 TPP sing 341 n n CM4 HM41 TPP sing 342 n n CM4 HM42 TPP sing 343 n n CM4 HM43 TPP sing 344 n n C6 C7 TPP sing 345 n n C6 H61 TPP sing 346 n n C6 H62 TPP sing 347 n n C7 O7 TPP sing 348 n n C7 H71 TPP sing 349 n n C7 H72 TPP sing 350 n n O7 PA TPP sing 351 n n PA O1A TPP doub 352 n n PA O2A TPP sing 353 n n PA O3A TPP sing 354 n n O2A HOA2 TPP sing 355 n n O3A PB TPP sing 356 n n PB O1B TPP doub 357 n n PB O2B TPP sing 358 n n PB O3B TPP sing 359 n n O2B HOB2 TPP sing 360 n n O3B HOB3 TPP sing 361 n n # _atom_sites.entry_id 1QPB _atom_sites.fract_transf_matrix[1][1] 0.006894 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004014 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008354 _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] 0.014236 _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 1 600 600 TPP TPP . D 3 MG A 1 601 601 MG MG . E 4 PYM A 1 602 602 PYM PYM . F 2 TPP B 1 600 600 TPP TPP . G 3 MG B 1 601 601 MG MG . H 4 PYM B 1 602 602 PYM PYM . I 5 HOH A 1 2001 2001 HOH HOH . I 5 HOH A 2 2002 2002 HOH HOH . I 5 HOH A 3 2003 2003 HOH HOH . I 5 HOH A 4 2004 2004 HOH HOH . I 5 HOH A 5 2005 2005 HOH HOH . I 5 HOH A 6 2006 2006 HOH HOH . I 5 HOH A 7 2007 2007 HOH HOH . I 5 HOH A 8 2008 2008 HOH HOH . I 5 HOH A 9 2009 2009 HOH HOH . I 5 HOH A 10 2010 2010 HOH HOH . I 5 HOH A 11 2011 2011 HOH HOH . I 5 HOH A 12 2012 2012 HOH HOH . I 5 HOH A 13 2013 2013 HOH HOH . I 5 HOH A 14 2014 2014 HOH HOH . I 5 HOH A 15 2015 2015 HOH HOH . I 5 HOH A 16 2016 2016 HOH HOH . I 5 HOH A 17 2017 2017 HOH HOH . I 5 HOH A 18 2018 2018 HOH HOH . I 5 HOH A 19 2019 2019 HOH HOH . I 5 HOH A 20 2020 2020 HOH HOH . I 5 HOH A 21 2021 2021 HOH HOH . I 5 HOH A 22 2022 2022 HOH HOH . I 5 HOH A 23 2023 2023 HOH HOH . I 5 HOH A 24 2024 2024 HOH HOH . I 5 HOH A 25 2025 2025 HOH HOH . I 5 HOH A 26 2026 2026 HOH HOH . I 5 HOH A 27 2027 2027 HOH HOH . I 5 HOH A 28 2028 2028 HOH HOH . I 5 HOH A 29 2029 2029 HOH HOH . I 5 HOH A 30 2030 2030 HOH HOH . I 5 HOH A 31 2031 2031 HOH HOH . I 5 HOH A 32 2032 2032 HOH HOH . I 5 HOH A 33 2033 2033 HOH HOH . I 5 HOH A 34 2034 2034 HOH HOH . I 5 HOH A 35 2035 2035 HOH HOH . I 5 HOH A 36 2036 2036 HOH HOH . I 5 HOH A 37 2037 2037 HOH HOH . I 5 HOH A 38 2038 2038 HOH HOH . I 5 HOH A 39 2039 2039 HOH HOH . I 5 HOH A 40 2040 2040 HOH HOH . I 5 HOH A 41 2041 2041 HOH HOH . I 5 HOH A 42 2042 2042 HOH HOH . I 5 HOH A 43 2043 2043 HOH HOH . I 5 HOH A 44 2044 2044 HOH HOH . I 5 HOH A 45 2045 2045 HOH HOH . I 5 HOH A 46 2046 2046 HOH HOH . I 5 HOH A 47 2047 2047 HOH HOH . I 5 HOH A 48 2048 2048 HOH HOH . I 5 HOH A 49 2049 2049 HOH HOH . I 5 HOH A 50 2050 2050 HOH HOH . I 5 HOH A 51 2051 2051 HOH HOH . I 5 HOH A 52 2052 2052 HOH HOH . I 5 HOH A 53 2053 2053 HOH HOH . I 5 HOH A 54 2054 2054 HOH HOH . I 5 HOH A 55 2055 2055 HOH HOH . I 5 HOH A 56 2056 2056 HOH HOH . I 5 HOH A 57 2057 2057 HOH HOH . I 5 HOH A 58 2058 2058 HOH HOH . I 5 HOH A 59 2059 2059 HOH HOH . I 5 HOH A 60 2060 2060 HOH HOH . I 5 HOH A 61 2061 2061 HOH HOH . I 5 HOH A 62 2062 2062 HOH HOH . I 5 HOH A 63 2063 2063 HOH HOH . I 5 HOH A 64 2064 2064 HOH HOH . I 5 HOH A 65 2065 2065 HOH HOH . I 5 HOH A 66 2066 2066 HOH HOH . I 5 HOH A 67 2067 2067 HOH HOH . I 5 HOH A 68 2068 2068 HOH HOH . I 5 HOH A 69 2069 2069 HOH HOH . I 5 HOH A 70 2070 2070 HOH HOH . I 5 HOH A 71 2071 2071 HOH HOH . I 5 HOH A 72 2072 2072 HOH HOH . I 5 HOH A 73 2073 2073 HOH HOH . I 5 HOH A 74 2074 2074 HOH HOH . I 5 HOH A 75 2075 2075 HOH HOH . I 5 HOH A 76 2076 2076 HOH HOH . I 5 HOH A 77 2077 2077 HOH HOH . I 5 HOH A 78 2078 2078 HOH HOH . I 5 HOH A 79 2079 2079 HOH HOH . I 5 HOH A 80 2080 2080 HOH HOH . I 5 HOH A 81 2081 2081 HOH HOH . I 5 HOH A 82 2082 2082 HOH HOH . I 5 HOH A 83 2083 2083 HOH HOH . I 5 HOH A 84 2084 2084 HOH HOH . I 5 HOH A 85 2085 2085 HOH HOH . J 5 HOH B 1 2001 2001 HOH HOH . J 5 HOH B 2 2002 2002 HOH HOH . J 5 HOH B 3 2003 2003 HOH HOH . J 5 HOH B 4 2004 2004 HOH HOH . J 5 HOH B 5 2005 2005 HOH HOH . J 5 HOH B 6 2006 2006 HOH HOH . J 5 HOH B 7 2007 2007 HOH HOH . J 5 HOH B 8 2008 2008 HOH HOH . J 5 HOH B 9 2009 2009 HOH HOH . J 5 HOH B 10 2010 2010 HOH HOH . J 5 HOH B 11 2011 2011 HOH HOH . J 5 HOH B 12 2012 2012 HOH HOH . J 5 HOH B 13 2013 2013 HOH HOH . J 5 HOH B 14 2014 2014 HOH HOH . J 5 HOH B 15 2015 2015 HOH HOH . J 5 HOH B 16 2016 2016 HOH HOH . J 5 HOH B 17 2017 2017 HOH HOH . J 5 HOH B 18 2018 2018 HOH HOH . J 5 HOH B 19 2019 2019 HOH HOH . J 5 HOH B 20 2020 2020 HOH HOH . J 5 HOH B 21 2021 2021 HOH HOH . J 5 HOH B 22 2022 2022 HOH HOH . J 5 HOH B 23 2023 2023 HOH HOH . J 5 HOH B 24 2024 2024 HOH HOH . J 5 HOH B 25 2025 2025 HOH HOH . J 5 HOH B 26 2026 2026 HOH HOH . J 5 HOH B 27 2027 2027 HOH HOH . J 5 HOH B 28 2028 2028 HOH HOH . J 5 HOH B 29 2029 2029 HOH HOH . J 5 HOH B 30 2030 2030 HOH HOH . J 5 HOH B 31 2031 2031 HOH HOH . J 5 HOH B 32 2032 2032 HOH HOH . J 5 HOH B 33 2033 2033 HOH HOH . J 5 HOH B 34 2034 2034 HOH HOH . J 5 HOH B 35 2035 2035 HOH HOH . J 5 HOH B 36 2036 2036 HOH HOH . J 5 HOH B 37 2037 2037 HOH HOH . J 5 HOH B 38 2038 2038 HOH HOH . J 5 HOH B 39 2039 2039 HOH HOH . J 5 HOH B 40 2040 2040 HOH HOH . J 5 HOH B 41 2041 2041 HOH HOH . J 5 HOH B 42 2042 2042 HOH HOH . J 5 HOH B 43 2043 2043 HOH HOH . J 5 HOH B 44 2044 2044 HOH HOH . J 5 HOH B 45 2045 2045 HOH HOH . J 5 HOH B 46 2046 2046 HOH HOH . J 5 HOH B 47 2047 2047 HOH HOH . J 5 HOH B 48 2048 2048 HOH HOH . J 5 HOH B 49 2049 2049 HOH HOH . J 5 HOH B 50 2050 2050 HOH HOH . J 5 HOH B 51 2051 2051 HOH HOH . J 5 HOH B 52 2052 2052 HOH HOH . J 5 HOH B 53 2053 2053 HOH HOH . J 5 HOH B 54 2054 2054 HOH HOH . J 5 HOH B 55 2055 2055 HOH HOH . J 5 HOH B 56 2056 2056 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 . . . F 2 99.126 35.345 9.02 1 20.82 ? N1' TPP 600 B 1 HETATM 2 C C2' TPP . . . F 2 98.087 34.887 9.788 1 22.78 ? C2' TPP 600 B 1 HETATM 3 C CM2 TPP . . . F 2 96.981 35.787 10.115 1 22.86 ? CM2 TPP 600 B 1 HETATM 4 N N3' TPP . . . F 2 97.975 33.625 10.059 1 21.87 ? N3' TPP 600 B 1 HETATM 5 C C4' TPP . . . F 2 99.016 32.746 9.803 1 23.24 ? C4' TPP 600 B 1 HETATM 6 N N4' TPP . . . F 2 98.753 31.48 10.129 1 23.12 ? N4' TPP 600 B 1 HETATM 7 C C5' TPP . . . F 2 100.236 33.179 9.122 1 21.78 ? C5' TPP 600 B 1 HETATM 8 C C6' TPP . . . F 2 100.191 34.501 8.691 1 22.05 ? C6' TPP 600 B 1 HETATM 9 C C7' TPP . . . F 2 101.38 32.257 8.682 1 19.91 ? C7' TPP 600 B 1 HETATM 10 N N3 TPP . . . F 2 102.248 31.634 9.794 1 15.82 ? N3 TPP 600 B 1 HETATM 11 C C2 TPP . . . F 2 102.076 30.37 10.185 1 13.34 ? C2 TPP 600 B 1 HETATM 12 S S1 TPP . . . F 2 103.091 29.968 11.425 1 17.15 ? S1 TPP 600 B 1 HETATM 13 C C5 TPP . . . F 2 103.748 31.492 11.463 1 11.29 ? C5 TPP 600 B 1 HETATM 14 C C4 TPP . . . F 2 103.249 32.291 10.491 1 14.23 ? C4 TPP 600 B 1 HETATM 15 C CM4 TPP . . . F 2 103.628 33.763 10.25 1 13.31 ? CM4 TPP 600 B 1 HETATM 16 C C6 TPP . . . F 2 104.733 31.781 12.49 1 13.4 ? C6 TPP 600 B 1 HETATM 17 C C7 TPP . . . F 2 104.395 31.301 13.969 1 14.3 ? C7 TPP 600 B 1 HETATM 18 O O7 TPP . . . F 2 105.712 31.253 14.62 1 14.61 ? O7 TPP 600 B 1 HETATM 19 P PA TPP . . . F 2 105.898 30.938 16.192 1 17.42 ? PA TPP 600 B 1 HETATM 20 O O1A TPP . . . F 2 107.281 31.389 16.295 1 18.75 ? O1A TPP 600 B 1 HETATM 21 O O2A TPP . . . F 2 104.981 31.516 17.193 1 12.64 ? O2A TPP 600 B 1 HETATM 22 O O3A TPP . . . F 2 105.806 29.331 16.065 1 19.62 ? O3A TPP 600 B 1 HETATM 23 P PB TPP . . . F 2 106.9 28.128 16.194 1 20.36 ? PB TPP 600 B 1 HETATM 24 O O1B TPP . . . F 2 106.769 27.797 17.642 1 19.51 ? O1B TPP 600 B 1 HETATM 25 O O2B TPP . . . F 2 106.429 27.075 15.253 1 20.38 ? O2B TPP 600 B 1 HETATM 26 O O3B TPP . . . F 2 108.168 28.761 15.764 1 16.25 ? O3B TPP 600 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #