data_7U1U # _model_server_result.job_id s9YAv0I3zqqsnnaX85q15w _model_server_result.datetime_utc '2024-11-27 22:19:24' _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 7u1u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":703}' # _entry.id 7U1U # _exptl.entry_id 7U1U _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 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 7U1U _cell.length_a 177.953 _cell.length_b 177.953 _cell.length_c 184.727 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U1U _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 _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' 10_666 -y+1,-x+1,-z+4/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 88.9765 154.111819 246.302667 # _struct_asym.details ? _struct_asym.entity_id 4 _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 covale ? covale1 A C PRO 254 A PRO 339 1_555 A N CSD 255 A CSD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CSD 255 A CSD 340 1_555 A N ASP 256 A ASP 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASP 453 A ASP 538 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc2 A OD1 ASN 480 A ASN 565 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc3 B MG MG . A MG 701 1_555 D O1A TPP . A TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc4 B MG MG . A MG 701 1_555 D O3B TPP . A TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _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 444 n y N1' C6' TPP sing 445 n y C2' CM2 TPP sing 446 n n C2' N3' TPP sing 447 n y CM2 HM21 TPP sing 448 n n CM2 HM22 TPP sing 449 n n CM2 HM23 TPP sing 450 n n N3' C4' TPP doub 451 n y C4' N4' TPP sing 452 n n C4' C5' TPP sing 453 n y N4' HN41 TPP sing 454 n n N4' HN42 TPP sing 455 n n C5' C6' TPP doub 456 n y C5' C7' TPP sing 457 n n C6' H6' TPP sing 458 n n C7' N3 TPP sing 459 n n C7' "H7'1" TPP sing 460 n n C7' "H7'2" TPP sing 461 n n N3 C2 TPP doub 462 n y N3 C4 TPP sing 463 n y C2 S1 TPP sing 464 n y C2 H2 TPP sing 465 n n S1 C5 TPP sing 466 n y C5 C4 TPP doub 467 n y C5 C6 TPP sing 468 n n C4 CM4 TPP sing 469 n n CM4 HM41 TPP sing 470 n n CM4 HM42 TPP sing 471 n n CM4 HM43 TPP sing 472 n n C6 C7 TPP sing 473 n n C6 H61 TPP sing 474 n n C6 H62 TPP sing 475 n n C7 O7 TPP sing 476 n n C7 H71 TPP sing 477 n n C7 H72 TPP sing 478 n n O7 PA TPP sing 479 n n PA O1A TPP doub 480 n n PA O2A TPP sing 481 n n PA O3A TPP sing 482 n n O2A HOA2 TPP sing 483 n n O3A PB TPP sing 484 n n PB O1B TPP doub 485 n n PB O2B TPP sing 486 n n PB O3B TPP sing 487 n n O2B HOB2 TPP sing 488 n n O3B HOB3 TPP sing 489 n n # _atom_sites.entry_id 7U1U _atom_sites.fract_transf_matrix[1][1] 0.005619 _atom_sites.fract_transf_matrix[1][2] 0.003244 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006489 _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] 0.005413 _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 1 701 699 MG MG . C 3 FAD A 1 702 701 FAD FAD . D 4 TPP A 1 703 801 TPP TPP . E 5 NHE A 1 704 901 NHE NHE . F 6 SO4 A 1 705 1001 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 . . . D 4 71.067 71.19 116.25 1 61.05 ? N1' TPP 703 A 1 HETATM 2 C C2' TPP . . . D 4 70.298 70.169 115.79 1 55.52 ? C2' TPP 703 A 1 HETATM 3 C CM2 TPP . . . D 4 69.797 69.138 116.732 1 57.75 ? CM2 TPP 703 A 1 HETATM 4 N N3' TPP . . . D 4 69.993 70.101 114.473 1 55.09 ? N3' TPP 703 A 1 HETATM 5 C C4' TPP . . . D 4 70.44 71.03 113.612 1 70.74 ? C4' TPP 703 A 1 HETATM 6 N N4' TPP . . . D 4 70.088 70.91 112.24 1 82.07 ? N4' TPP 703 A 1 HETATM 7 C C5' TPP . . . D 4 71.226 72.079 114.08 1 66.6 ? C5' TPP 703 A 1 HETATM 8 C C6' TPP . . . D 4 71.526 72.132 115.415 1 67.85 ? C6' TPP 703 A 1 HETATM 9 C C7' TPP . . . D 4 71.769 73.154 113.167 1 81.52 ? C7' TPP 703 A 1 HETATM 10 N N3 TPP . . . D 4 72.797 72.552 112.309 1 79.35 ? N3 TPP 703 A 1 HETATM 11 C C2 TPP . . . D 4 72.486 72.243 111.06 1 61.04 ? C2 TPP 703 A 1 HETATM 12 S S1 TPP . . . D 4 73.848 71.528 110.237 1 73.04 ? S1 TPP 703 A 1 HETATM 13 C C5 TPP . . . D 4 74.828 71.684 111.682 1 66.6 ? C5 TPP 703 A 1 HETATM 14 C C4 TPP . . . D 4 74.045 72.271 112.689 1 75.89 ? C4 TPP 703 A 1 HETATM 15 C CM4 TPP . . . D 4 74.614 72.537 114.055 1 52.71 ? CM4 TPP 703 A 1 HETATM 16 C C6 TPP . . . D 4 76.276 71.257 111.814 1 66.82 ? C6 TPP 703 A 1 HETATM 17 C C7 TPP . . . D 4 76.401 69.75 111.783 1 64.24 ? C7 TPP 703 A 1 HETATM 18 O O7 TPP . . . D 4 77.726 69.424 111.525 1 77.37 ? O7 TPP 703 A 1 HETATM 19 P PA TPP . . . D 4 77.919 67.886 111.3 1 71.59 ? PA TPP 703 A 1 HETATM 20 O O1A TPP . . . D 4 79.229 67.449 111.881 1 55.67 ? O1A TPP 703 A 1 HETATM 21 O O2A TPP . . . D 4 76.813 67.103 111.981 1 50.89 ? O2A TPP 703 A 1 HETATM 22 O O3A TPP . . . D 4 77.857 67.622 109.753 1 86.93 ? O3A TPP 703 A 1 HETATM 23 P PB TPP . . . D 4 78.911 68.41 108.908 1 77.96 ? PB TPP 703 A 1 HETATM 24 O O1B TPP . . . D 4 79.377 67.545 107.75 1 59.37 ? O1B TPP 703 A 1 HETATM 25 O O2B TPP . . . D 4 78.299 69.661 108.358 1 47.45 ? O2B TPP 703 A 1 HETATM 26 O O3B TPP . . . D 4 80.117 68.787 109.754 1 77.06 ? O3B TPP 703 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #