data_4NYG # _model_server_result.job_id MjV9ocVnqBHBbRJjmuVhBw _model_server_result.datetime_utc '2024-11-05 23:31:48' _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 4nyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":101}' # _entry.id 4NYG # _exptl.entry_id 4NYG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.355 _entity.id 2 _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 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 4NYG _cell.length_a 61.503 _cell.length_b 61.503 _cell.length_c 103.935 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYG _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 O3' C 82 A C 90 1_555 A P A23 83 A A23 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? metalc ? metalc1 A O6 G 9 A G 17 1_555 D MG MG . A MG 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc2 A OP2 A 27 A A 35 1_555 F MG MG . A MG 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc3 A OP1 G 32 A G 40 1_555 E MG MG . A MG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc4 C MG MG . A MG 102 1_555 I O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc5 H MG MG . A MG 107 1_555 I O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 9 1_555 A N3 C 82 A C 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 9 1_555 A O2 C 82 A C 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 9 1_555 A N4 C 82 A C 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 2 A C 10 1_555 A N1 G 81 A G 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 2 A C 10 1_555 A O6 G 81 A G 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 2 A C 10 1_555 A N2 G 81 A G 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 3 A G 11 1_555 A N3 C 80 A C 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 3 A G 11 1_555 A O2 C 80 A C 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 3 A G 11 1_555 A N4 C 80 A C 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 A 4 A A 12 1_555 A N3 U 79 A U 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 A 4 A A 12 1_555 A O4 U 79 A U 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog12 A O2 C 5 A C 13 1_555 A N2 G 78 A G 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 C 7 A C 15 1_555 A N1 G 43 A G 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 C 7 A C 15 1_555 A O6 G 43 A G 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 C 7 A C 15 1_555 A N2 G 43 A G 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 G 8 A G 16 1_555 A N3 C 42 A C 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 G 8 A G 16 1_555 A O2 C 42 A C 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 G 8 A G 16 1_555 A N4 C 42 A C 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog19 A N2 G 8 A G 16 1_555 A N3 A 76 A A 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 G 9 A G 17 1_555 A N3 C 41 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 G 9 A G 17 1_555 A O2 C 41 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 G 9 A G 17 1_555 A N4 C 41 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog23 A N2 G 9 A G 17 1_555 A N3 A 48 A A 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog24 A N1 G 10 A G 18 1_555 A O2 C 40 A C 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_4_PAIR hydrog25 A N2 G 11 A G 19 1_555 A N3 G 34 A G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_4_PAIR hydrog26 A N3 G 11 A G 19 1_555 A N2 G 34 A G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog27 A N1 G 11 A G 19 1_555 A N1 A 39 A A 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog28 A O6 G 11 A G 19 1_555 A N6 A 39 A A 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 U 12 A U 20 1_555 A N1 A 37 A A 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O4 U 12 A U 20 1_555 A N6 A 37 A A 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 G 13 A G 21 1_555 A N3 C 30 A C 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N2 G 13 A G 21 1_555 A O2 C 30 A C 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O6 G 13 A G 21 1_555 A N4 C 30 A C 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog34 A N2 G 13 A G 21 1_555 A O2 U 63 A U 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog35 A O2 C 14 A C 22 1_555 A N2 G 29 A G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N3 C 15 A C 23 1_555 A N1 G 28 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N4 C 15 A C 23 1_555 A O6 G 28 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A O2 C 15 A C 23 1_555 A N2 G 28 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog39 A N3 U 31 A U 39 1_555 A N7 A 35 A A 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog40 A O2 U 31 A U 39 1_555 A N6 A 35 A A 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog41 A N7 A 45 A A 53 1_555 A N6 A 76 A A 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog42 A N6 A 48 A A 56 1_555 A N3 G 75 A G 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog43 A N7 A 48 A A 56 1_555 A N2 G 75 A G 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A N3 C 49 A C 57 1_555 A N1 G 74 A G 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 A N4 C 49 A C 57 1_555 A O6 G 74 A G 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 A O2 C 49 A C 57 1_555 A N2 G 74 A G 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 A N3 C 50 A C 58 1_555 A N1 G 73 A G 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 A N4 C 50 A C 58 1_555 A O6 G 73 A G 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 A O2 C 50 A C 58 1_555 A N2 G 73 A G 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog50 A N3 U 51 A U 59 1_555 A N1 A 72 A A 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog51 A O4 U 51 A U 59 1_555 A N6 A 72 A A 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog52 A N1 G 52 A G 60 1_555 A N3 C 69 A C 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog53 A N2 G 58 A G 66 1_555 A N3 C 65 A C 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog54 A N1 G 58 A G 66 1_555 A N3 C 66 A C 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 195 n n CM2 HM21 VIB sing 196 n n CM2 HM22 VIB sing 197 n n CM2 HM23 VIB sing 198 n n N4A C4A VIB sing 199 n n N4A H4A1 VIB sing 200 n n N4A H4A2 VIB sing 201 n n CM4 C4 VIB sing 202 n n CM4 HM41 VIB sing 203 n n CM4 HM42 VIB sing 204 n n CM4 HM43 VIB sing 205 n n O1 C7 VIB sing 206 n n O1 HO1 VIB sing 207 n n C7 C6 VIB sing 208 n n C7 HC71 VIB sing 209 n n C7 HC72 VIB sing 210 n n C6 C5 VIB sing 211 n n C6 HC61 VIB sing 212 n n C6 HC62 VIB sing 213 n n C2 S1 VIB sing 214 n y C2 N3 VIB doub 215 n y C2 HC2 VIB sing 216 n n S1 C5 VIB sing 217 n y C5 C4 VIB doub 218 n y C4 N3 VIB sing 219 n y N3 C7A VIB sing 220 n n C7A C5A VIB sing 221 n n C7A H7A1 VIB sing 222 n n C7A H7A2 VIB sing 223 n n C4A N3A VIB sing 224 n y C4A C5A VIB doub 225 n y N3A C2A VIB doub 226 n y C2A N1A VIB sing 227 n y N1A C6A VIB doub 228 n y C6A C5A VIB sing 229 n y C6A H6AC VIB sing 230 n n # _atom_sites.entry_id 4NYG _atom_sites.fract_transf_matrix[1][1] 0.016259 _atom_sites.fract_transf_matrix[1][2] 0.009387 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018775 _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] 0.009621 _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 VIB A 1 101 200 VIB VIB . C 3 MG A 1 102 102 MG MG . D 3 MG A 1 103 103 MG MG . E 3 MG A 1 104 104 MG MG . F 3 MG A 1 105 105 MG MG . G 3 MG A 1 106 108 MG MG . H 3 MG A 1 107 109 MG MG . I 4 HOH A 1 201 110 HOH HOH . I 4 HOH A 2 202 107 HOH HOH . I 4 HOH A 3 203 111 HOH HOH . I 4 HOH A 4 204 101 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 . . . B 2 -12.533 15.287 2.753 1 81.61 ? CM2 VIB 101 A 1 HETATM 2 N N4A VIB . . . B 2 -9.058 11.921 2.397 1 89.63 ? N4A VIB 101 A 1 HETATM 3 C CM4 VIB . . . B 2 -4.496 14.243 3.666 1 98.82 ? CM4 VIB 101 A 1 HETATM 4 O O1 VIB . . . B 2 -0.293 16.891 2.065 1 102.42 ? O1 VIB 101 A 1 HETATM 5 C C7 VIB . . . B 2 -1.555 16.482 1.556 1 101.3 ? C7 VIB 101 A 1 HETATM 6 C C6 VIB . . . B 2 -2.618 16.523 2.671 1 102.31 ? C6 VIB 101 A 1 HETATM 7 C C2 VIB . . . B 2 -6.137 15.701 0.634 1 101.11 ? C2 VIB 101 A 1 HETATM 8 S S1 VIB . . . B 2 -4.752 16.743 0.64 1 103.74 ? S1 VIB 101 A 1 HETATM 9 C C5 VIB . . . B 2 -3.935 16.08 2.073 1 101.14 ? C5 VIB 101 A 1 HETATM 10 C C4 VIB . . . B 2 -4.813 15.093 2.447 1 99.61 ? C4 VIB 101 A 1 HETATM 11 N N3 VIB . . . B 2 -5.939 14.921 1.689 1 98.25 ? N3 VIB 101 A 1 HETATM 12 C C7A VIB . . . B 2 -6.947 13.85 2.013 1 91.66 ? C7A VIB 101 A 1 HETATM 13 C C4A VIB . . . B 2 -9.412 13.27 2.38 1 88.05 ? C4A VIB 101 A 1 HETATM 14 N N3A VIB . . . B 2 -10.72 13.632 2.553 1 85.51 ? N3A VIB 101 A 1 HETATM 15 C C2A VIB . . . B 2 -11.084 14.917 2.543 1 84.72 ? C2A VIB 101 A 1 HETATM 16 N N1A VIB . . . B 2 -10.176 15.88 2.36 1 85.51 ? N1A VIB 101 A 1 HETATM 17 C C6A VIB . . . B 2 -8.859 15.597 2.185 1 86.27 ? C6A VIB 101 A 1 HETATM 18 C C5A VIB . . . B 2 -8.415 14.27 2.192 1 87.62 ? C5A VIB 101 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #