data_7U25 # _model_server_result.job_id 0U5gWXHwWuHg0soPGg1cxw _model_server_result.datetime_utc '2025-02-17 15:55:42' _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 7u25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":704}' # _entry.id 7U25 # _exptl.entry_id 7U25 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 440.306 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN 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 120 _cell.entry_id 7U25 _cell.length_a 179.952 _cell.length_b 179.952 _cell.length_c 185.472 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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 _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' 12_544 x,x-y-1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 89.976 -155.843003 -61.824 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 A OD1 ASP 453 A ASP 538 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 A OD1 ASN 480 A ASN 565 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc3 A O HIS 482 A HIS 567 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc4 B MG MG . A MG 701 1_555 E O13 TZD . A TZD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc5 B MG MG . A MG 701 1_555 E O23 TZD . A TZD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _chem_comp.formula 'C12 H18 N4 O8 P2 S' _chem_comp.formula_weight 440.306 _chem_comp.id TZD _chem_comp.mon_nstd_flag . _chem_comp.name '2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'THIAMIN THIAZOLONE DIPHOSPHATE' # 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' TZD doub 532 n y N1' C6' TZD sing 533 n y C2' C2A TZD sing 534 n n C2' N3' TZD sing 535 n y C2A H2A1 TZD sing 536 n n C2A H2A2 TZD sing 537 n n C2A H2A3 TZD sing 538 n n N3' C4' TZD doub 539 n y C4' N4' TZD sing 540 n n C4' C5' TZD sing 541 n y N4' "H4'1" TZD sing 542 n n N4' "H4'2" TZD sing 543 n n C5' C6' TZD doub 544 n y C5' C35 TZD sing 545 n n C6' H6' TZD sing 546 n n C35 N3 TZD sing 547 n n C35 H351 TZD sing 548 n n C35 H352 TZD sing 549 n n N3 C2 TZD sing 550 n y N3 C4 TZD sing 551 n y C2 OC2 TZD doub 552 n n C2 S1 TZD sing 553 n y S1 C5 TZD sing 554 n y C5 C4 TZD doub 555 n y C5 C5A TZD sing 556 n n C4 C4A TZD sing 557 n n C4A H4A1 TZD sing 558 n n C4A H4A2 TZD sing 559 n n C4A H4A3 TZD sing 560 n n C5A C5B TZD sing 561 n n C5A H5A1 TZD sing 562 n n C5A H5A2 TZD sing 563 n n C5B O5G TZD sing 564 n n C5B H5B1 TZD sing 565 n n C5B H5B2 TZD sing 566 n n O5G P1 TZD sing 567 n n P1 O11 TZD sing 568 n n P1 O12 TZD doub 569 n n P1 O13 TZD sing 570 n n O11 P2 TZD sing 571 n n O13 H13 TZD sing 572 n n P2 O21 TZD sing 573 n n P2 O22 TZD doub 574 n n P2 O23 TZD sing 575 n n O21 H21 TZD sing 576 n n O23 H23 TZD sing 577 n n # _atom_sites.entry_id 7U25 _atom_sites.fract_transf_matrix[1][1] 0.005557 _atom_sites.fract_transf_matrix[1][2] 0.003208 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006417 _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] 0.005392 _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 B 2 MG A 1 701 701 MG MG . C 3 6QL A 1 702 801 6QL 6QL . D 4 FAD A 1 703 1201 FAD FAD . E 5 TZD A 1 704 1301 TZD TZD . F 6 NHE A 1 705 1701 NHE NHE . G 7 SO4 A 1 706 1801 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' TZD . . . E 5 71.772 -72.056 -24.099 0.89 68.23 ? N1' TZD 704 A 1 HETATM 2 C C2' TZD . . . E 5 70.961 -71.101 -23.59 0.89 68.77 ? C2' TZD 704 A 1 HETATM 3 C C2A TZD . . . E 5 70.402 -70.007 -24.497 0.89 67.64 ? C2A TZD 704 A 1 HETATM 4 N N3' TZD . . . E 5 70.646 -71.114 -22.275 0.89 68.35 ? N3' TZD 704 A 1 HETATM 5 C C4' TZD . . . E 5 71.129 -72.059 -21.487 0.89 70.72 ? C4' TZD 704 A 1 HETATM 6 N N4' TZD . . . E 5 70.776 -72.057 -20.08 0.89 69.4 ? N4' TZD 704 A 1 HETATM 7 C C5' TZD . . . E 5 71.941 -73.019 -21.997 0.89 69.6 ? C5' TZD 704 A 1 HETATM 8 C C6' TZD . . . E 5 72.255 -73.003 -23.314 0.89 70.63 ? C6' TZD 704 A 1 HETATM 9 C C35 TZD . . . E 5 72.51 -74.119 -21.098 0.89 71.26 ? C35 TZD 704 A 1 HETATM 10 N N3 TZD . . . E 5 73.507 -73.551 -20.208 0.89 78.84 ? N3 TZD 704 A 1 HETATM 11 C C2 TZD . . . E 5 73.221 -73.303 -18.865 0.89 99.21 ? C2 TZD 704 A 1 HETATM 12 O OC2 TZD . . . E 5 72.009 -73.544 -18.205 0.89 87.69 ? OC2 TZD 704 A 1 HETATM 13 S S1 TZD . . . E 5 74.58 -72.668 -18.218 0.89 81.81 ? S1 TZD 704 A 1 HETATM 14 C C5 TZD . . . E 5 75.693 -72.618 -19.477 0.89 70.73 ? C5 TZD 704 A 1 HETATM 15 C C4 TZD . . . E 5 74.959 -73.186 -20.713 0.89 76.72 ? C4 TZD 704 A 1 HETATM 16 C C4A TZD . . . E 5 75.528 -73.361 -22.12 0.89 67.99 ? C4A TZD 704 A 1 HETATM 17 C C5A TZD . . . E 5 77.129 -72.104 -19.402 0.89 73.13 ? C5A TZD 704 A 1 HETATM 18 C C5B TZD . . . E 5 77.107 -70.578 -19.387 0.89 62.47 ? C5B TZD 704 A 1 HETATM 19 O O5G TZD . . . E 5 78.381 -70.078 -19.676 0.89 63.2 ? O5G TZD 704 A 1 HETATM 20 P P1 TZD . . . E 5 78.783 -68.581 -19.112 0.89 59.33 ? P1 TZD 704 A 1 HETATM 21 O O11 TZD . . . E 5 78.68 -68.567 -17.467 0.89 78.93 ? O11 TZD 704 A 1 HETATM 22 O O12 TZD . . . E 5 77.836 -67.553 -19.683 0.89 57.4 -1 O12 TZD 704 A 1 HETATM 23 O O13 TZD . . . E 5 80.194 -68.249 -19.533 0.89 71.56 ? O13 TZD 704 A 1 HETATM 24 P P2 TZD . . . E 5 79.685 -69.418 -16.477 0.89 67.64 ? P2 TZD 704 A 1 HETATM 25 O O21 TZD . . . E 5 80.3 -68.484 -15.461 0.89 69.81 ? O21 TZD 704 A 1 HETATM 26 O O22 TZD . . . E 5 78.901 -70.49 -15.76 0.89 62.02 -1 O22 TZD 704 A 1 HETATM 27 O O23 TZD . . . E 5 80.778 -70.054 -17.302 0.89 74.91 -1 O23 TZD 704 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #