data_1SBR # _model_server_result.job_id -veuvJtrgB9QW4bPRfzVfw _model_server_result.datetime_utc '2024-11-17 16:12:55' _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 1sbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1SBR # _exptl.entry_id 1SBR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.355 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM _entity.pdbx_number_of_molecules 4 _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 1SBR _cell.length_a 58.82 _cell.length_b 82.49 _cell.length_c 86.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _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,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 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 covale ? covale1 A C PRO 19 A PRO 19 1_555 A N MSE 20 A MSE 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 20 A MSE 20 1_555 A N THR 21 A THR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C VAL 77 A VAL 77 1_555 A N MSE 78 A MSE 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale4 A C MSE 78 A MSE 78 1_555 A N ASN 79 A ASN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale5 A C PRO 123 A PRO 123 1_555 A N MSE 124 A MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 124 A MSE 124 1_555 A N ASN 125 A ASN 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C TYR 129 A TYR 129 1_555 A N MSE 130 A MSE 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale8 A C MSE 130 A MSE 130 1_555 A N GLY 131 A GLY 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 A C ILE 133 A ILE 133 1_555 A N MSE 134 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 A C MSE 134 A MSE 134 1_555 A N GLU 135 A GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C ARG 172 A ARG 172 1_555 A N MSE 173 A MSE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C MSE 173 A MSE 173 1_555 A N ALA 174 A ALA 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C THR 182 A THR 182 1_555 A N MSE 183 A MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale14 A C MSE 183 A MSE 183 1_555 A N THR 184 A THR 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale15 B C PRO 19 B PRO 19 1_555 B N MSE 20 B MSE 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 20 B MSE 20 1_555 B N THR 21 B THR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale17 B C VAL 77 B VAL 77 1_555 B N MSE 78 B MSE 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 B C MSE 78 B MSE 78 1_555 B N ASN 79 B ASN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale19 B C PRO 123 B PRO 123 1_555 B N MSE 124 B MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale20 B C MSE 124 B MSE 124 1_555 B N ASN 125 B ASN 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale21 B C TYR 129 B TYR 129 1_555 B N MSE 130 B MSE 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 B C MSE 130 B MSE 130 1_555 B N GLY 131 B GLY 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale23 B C ILE 133 B ILE 133 1_555 B N MSE 134 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 B C MSE 134 B MSE 134 1_555 B N GLU 135 B GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale25 B C ARG 172 B ARG 172 1_555 B N MSE 173 B MSE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale26 B C MSE 173 B MSE 173 1_555 B N ALA 174 B ALA 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale27 B C THR 182 B THR 182 1_555 B N MSE 183 B MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale28 B C MSE 183 B MSE 183 1_555 B N THR 184 B THR 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A O ALA 33 A ALA 33 1_555 C CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc2 A O THR 35 A THR 35 1_555 C CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 C CA CA . A CA 801 1_555 H O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc4 C CA CA . A CA 801 1_555 B O ALA 33 B ALA 33 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc5 C CA CA . A CA 801 1_555 B O THR 35 B THR 35 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc6 C CA CA . A CA 801 1_555 I O HOH . B HOH 803 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? # _chem_comp.formula 'C12 H17 N4 O S 1' _chem_comp.formula_weight 265.355 _chem_comp.id VIB _chem_comp.mon_nstd_flag . _chem_comp.name 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'THIAMIN;VITAMIN B1' # 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 CM2 C2A VIB sing 395 n n CM2 HM21 VIB sing 396 n n CM2 HM22 VIB sing 397 n n CM2 HM23 VIB sing 398 n n N4A C4A VIB sing 399 n n N4A H4A1 VIB sing 400 n n N4A H4A2 VIB sing 401 n n CM4 C4 VIB sing 402 n n CM4 HM41 VIB sing 403 n n CM4 HM42 VIB sing 404 n n CM4 HM43 VIB sing 405 n n O1 C7 VIB sing 406 n n O1 HO1 VIB sing 407 n n C7 C6 VIB sing 408 n n C7 HC71 VIB sing 409 n n C7 HC72 VIB sing 410 n n C6 C5 VIB sing 411 n n C6 HC61 VIB sing 412 n n C6 HC62 VIB sing 413 n n C2 S1 VIB sing 414 n y C2 N3 VIB doub 415 n y C2 HC2 VIB sing 416 n n S1 C5 VIB sing 417 n y C5 C4 VIB doub 418 n y C4 N3 VIB sing 419 n y N3 C7A VIB sing 420 n n C7A C5A VIB sing 421 n n C7A H7A1 VIB sing 422 n n C7A H7A2 VIB sing 423 n n C4A N3A VIB sing 424 n y C4A C5A VIB doub 425 n y N3A C2A VIB doub 426 n y C2A N1A VIB sing 427 n y N1A C6A VIB doub 428 n y C6A C5A VIB sing 429 n y C6A H6AC VIB sing 430 n n # _atom_sites.entry_id 1SBR _atom_sites.fract_transf_matrix[1][1] 0.017001 _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] 0.012123 _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] 0.011613 _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 CA A 1 801 801 CA CA . D 3 VIB A 1 501 501 VIB VIB . E 3 VIB A 1 502 502 VIB VIB . F 3 VIB B 1 503 503 VIB VIB . G 3 VIB B 1 504 504 VIB VIB . H 4 HOH A 1 802 802 HOH HOH . H 4 HOH A 2 805 805 HOH HOH . H 4 HOH A 3 810 810 HOH HOH . H 4 HOH A 4 811 811 HOH HOH . H 4 HOH A 5 813 813 HOH HOH . H 4 HOH A 6 815 815 HOH HOH . H 4 HOH A 7 817 817 HOH HOH . H 4 HOH A 8 818 818 HOH HOH . H 4 HOH A 9 823 823 HOH HOH . H 4 HOH A 10 824 824 HOH HOH . H 4 HOH A 11 827 827 HOH HOH . H 4 HOH A 12 828 828 HOH HOH . H 4 HOH A 13 830 830 HOH HOH . H 4 HOH A 14 831 831 HOH HOH . H 4 HOH A 15 832 832 HOH HOH . H 4 HOH A 16 833 833 HOH HOH . H 4 HOH A 17 834 834 HOH HOH . H 4 HOH A 18 836 836 HOH HOH . H 4 HOH A 19 841 841 HOH HOH . H 4 HOH A 20 842 842 HOH HOH . H 4 HOH A 21 844 844 HOH HOH . H 4 HOH A 22 846 846 HOH HOH . H 4 HOH A 23 849 849 HOH HOH . H 4 HOH A 24 850 850 HOH HOH . H 4 HOH A 25 853 853 HOH HOH . H 4 HOH A 26 854 854 HOH HOH . H 4 HOH A 27 855 855 HOH HOH . H 4 HOH A 28 858 858 HOH HOH . H 4 HOH A 29 860 860 HOH HOH . H 4 HOH A 30 862 862 HOH HOH . H 4 HOH A 31 864 864 HOH HOH . H 4 HOH A 32 865 865 HOH HOH . H 4 HOH A 33 867 867 HOH HOH . H 4 HOH A 34 868 868 HOH HOH . H 4 HOH A 35 871 871 HOH HOH . H 4 HOH A 36 872 872 HOH HOH . H 4 HOH A 37 873 873 HOH HOH . H 4 HOH A 38 874 874 HOH HOH . H 4 HOH A 39 876 876 HOH HOH . H 4 HOH A 40 877 877 HOH HOH . I 4 HOH B 1 803 803 HOH HOH . I 4 HOH B 2 804 804 HOH HOH . I 4 HOH B 3 806 806 HOH HOH . I 4 HOH B 4 807 807 HOH HOH . I 4 HOH B 5 808 808 HOH HOH . I 4 HOH B 6 809 809 HOH HOH . I 4 HOH B 7 812 812 HOH HOH . I 4 HOH B 8 814 814 HOH HOH . I 4 HOH B 9 816 816 HOH HOH . I 4 HOH B 10 819 819 HOH HOH . I 4 HOH B 11 820 820 HOH HOH . I 4 HOH B 12 821 821 HOH HOH . I 4 HOH B 13 822 822 HOH HOH . I 4 HOH B 14 825 825 HOH HOH . I 4 HOH B 15 826 826 HOH HOH . I 4 HOH B 16 829 829 HOH HOH . I 4 HOH B 17 835 835 HOH HOH . I 4 HOH B 18 837 837 HOH HOH . I 4 HOH B 19 838 838 HOH HOH . I 4 HOH B 20 839 839 HOH HOH . I 4 HOH B 21 840 840 HOH HOH . I 4 HOH B 22 843 843 HOH HOH . I 4 HOH B 23 845 845 HOH HOH . I 4 HOH B 24 847 847 HOH HOH . I 4 HOH B 25 848 848 HOH HOH . I 4 HOH B 26 851 851 HOH HOH . I 4 HOH B 27 852 852 HOH HOH . I 4 HOH B 28 856 856 HOH HOH . I 4 HOH B 29 857 857 HOH HOH . I 4 HOH B 30 859 859 HOH HOH . I 4 HOH B 31 861 861 HOH HOH . I 4 HOH B 32 863 863 HOH HOH . I 4 HOH B 33 866 866 HOH HOH . I 4 HOH B 34 869 869 HOH HOH . I 4 HOH B 35 870 870 HOH HOH . I 4 HOH B 36 875 875 HOH HOH . I 4 HOH B 37 878 878 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 C CM2 VIB . . . D 3 11.651 41.944 4.241 1 37.02 ? CM2 VIB 501 A 1 HETATM 2 N N4A VIB . . . D 3 14.765 43.937 7.266 1 39.47 ? N4A VIB 501 A 1 HETATM 3 C CM4 VIB . . . D 3 16.056 46.27 3.044 1 42.94 ? CM4 VIB 501 A 1 HETATM 4 O O1 VIB . . . D 3 19.478 44.775 1.579 1 61.6 ? O1 VIB 501 A 1 HETATM 5 C C7 VIB . . . D 3 19.288 44.642 2.973 1 55.9 ? C7 VIB 501 A 1 HETATM 6 C C6 VIB . . . D 3 19.185 46.063 3.472 1 54.22 ? C6 VIB 501 A 1 HETATM 7 C C2 VIB . . . D 3 17.044 46.203 6.529 1 50.68 ? C2 VIB 501 A 1 HETATM 8 S S1 VIB . . . D 3 18.685 46.075 6.115 1 52.03 ? S1 VIB 501 A 1 HETATM 9 C C5 VIB . . . D 3 18.124 46.115 4.553 1 51.6 ? C5 VIB 501 A 1 HETATM 10 C C4 VIB . . . D 3 16.781 46.228 4.375 1 49.14 ? C4 VIB 501 A 1 HETATM 11 N N3 VIB . . . D 3 16.174 46.273 5.545 1 49.74 ? N3 VIB 501 A 1 HETATM 12 C C7A VIB . . . D 3 14.856 46.342 5.747 1 46.07 ? C7A VIB 501 A 1 HETATM 13 C C4A VIB . . . D 3 14.062 44.114 6.135 1 40.33 ? C4A VIB 501 A 1 HETATM 14 N N3A VIB . . . D 3 13.282 43.095 5.796 1 39.11 ? N3A VIB 501 A 1 HETATM 15 C C2A VIB . . . D 3 12.596 43.093 4.547 1 39.21 ? C2A VIB 501 A 1 HETATM 16 N N1A VIB . . . D 3 12.543 44.372 3.858 1 41.05 ? N1A VIB 501 A 1 HETATM 17 C C6A VIB . . . D 3 13.34 45.36 4.273 1 41.03 ? C6A VIB 501 A 1 HETATM 18 C C5A VIB . . . D 3 14.073 45.264 5.41 1 42.18 ? C5A VIB 501 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #