data_1TO9 # _model_server_result.job_id utOT3oXCVq5TQJRoPj9Wtg _model_server_result.datetime_utc '2025-04-27 20:57:26' _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 1to9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1TO9 # _exptl.entry_id 1TO9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 139.155 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE _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 90 _cell.angle_gamma 90 _cell.entry_id 1TO9 _cell.length_a 58.38 _cell.length_b 58.38 _cell.length_c 296.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TO9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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 1 1 A,B,C,D,E,F 2 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D 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 ARG 94 A ARG 70 1_555 A N MSE 95 A MSE 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 95 A MSE 71 1_555 A N ALA 96 A ALA 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C GLU 106 A GLU 82 1_555 A N MSE 107 A MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 107 A MSE 83 1_555 A N ALA 108 A ALA 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale5 A C HIS 139 A HIS 115 1_555 A N MSE 140 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale6 A C MSE 140 A MSE 116 1_555 A N TYR 141 A TYR 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C LYS 217 A LYS 193 1_555 A N MSE 218 A MSE 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 A C MSE 218 A MSE 194 1_555 A N LYS 219 A LYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 A C GLY 234 A GLY 210 1_555 A N MSE 235 A MSE 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale10 A C MSE 235 A MSE 211 1_555 A N ALA 236 A ALA 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 B C ALA 24 B ALA 0 1_555 B N MSE 25 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale12 B C MSE 25 B MSE 1 1_555 B N LYS 26 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale13 B C ARG 94 B ARG 70 1_555 B N MSE 95 B MSE 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 B C MSE 95 B MSE 71 1_555 B N ALA 96 B ALA 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale15 B C GLU 106 B GLU 82 1_555 B N MSE 107 B MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale16 B C MSE 107 B MSE 83 1_555 B N ALA 108 B ALA 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C HIS 139 B HIS 115 1_555 B N MSE 140 B MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale18 B C MSE 140 B MSE 116 1_555 B N TYR 141 B TYR 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale19 B C HIS 172 B HIS 148 1_555 B N CSD 173 B CSD 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale20 B C CSD 173 B CSD 149 1_555 B N ASP 174 B ASP 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale21 B C LYS 217 B LYS 193 1_555 B N MSE 218 B MSE 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale22 B C MSE 218 B MSE 194 1_555 B N LYS 219 B LYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale23 B C GLY 234 B GLY 210 1_555 B N MSE 235 B MSE 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale24 B C MSE 235 B MSE 211 1_555 B N ALA 236 B ALA 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _chem_comp.formula 'C6 H9 N3 O' _chem_comp.formula_weight 139.155 _chem_comp.id HMH _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE _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 CM2 C2A HMH sing 165 n n CM2 HCM1 HMH sing 166 n n CM2 HCM2 HMH sing 167 n n CM2 HCM3 HMH sing 168 n n N1A C2A HMH doub 169 n y N1A C6A HMH sing 170 n y C2A N3A HMH sing 171 n y N3A C4A HMH doub 172 n y C4A N4A HMH sing 173 n n C4A C5A HMH sing 174 n y N4A HN41 HMH sing 175 n n N4A HN42 HMH sing 176 n n C5A C6A HMH doub 177 n y C5A C7A HMH sing 178 n n C6A HC6 HMH sing 179 n n C7A O1 HMH sing 180 n n C7A HC71 HMH sing 181 n n C7A HC72 HMH sing 182 n n O1 HO1 HMH sing 183 n n # _atom_sites.entry_id 1TO9 _atom_sites.fract_transf_matrix[1][1] 0.017129 _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] 0.017129 _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] 0.003376 _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 3 HMH A 1 301 301 HMH HMH . D 3 HMH B 1 302 302 HMH HMH . E 4 HOH A 1 302 1 HOH HOH . E 4 HOH A 2 303 10 HOH HOH . E 4 HOH A 3 304 18 HOH HOH . E 4 HOH A 4 305 19 HOH HOH . E 4 HOH A 5 306 23 HOH HOH . E 4 HOH A 6 307 25 HOH HOH . E 4 HOH A 7 308 27 HOH HOH . E 4 HOH A 8 309 28 HOH HOH . E 4 HOH A 9 310 29 HOH HOH . F 4 HOH B 1 303 2 HOH HOH . F 4 HOH B 2 304 3 HOH HOH . F 4 HOH B 3 305 4 HOH HOH . F 4 HOH B 4 306 5 HOH HOH . F 4 HOH B 5 307 6 HOH HOH . F 4 HOH B 6 308 7 HOH HOH . F 4 HOH B 7 309 8 HOH HOH . F 4 HOH B 8 310 9 HOH HOH . F 4 HOH B 9 311 11 HOH HOH . F 4 HOH B 10 312 12 HOH HOH . F 4 HOH B 11 313 13 HOH HOH . F 4 HOH B 12 314 14 HOH HOH . F 4 HOH B 13 315 15 HOH HOH . F 4 HOH B 14 316 16 HOH HOH . F 4 HOH B 15 317 17 HOH HOH . F 4 HOH B 16 318 20 HOH HOH . F 4 HOH B 17 319 21 HOH HOH . F 4 HOH B 18 320 22 HOH HOH . F 4 HOH B 19 321 24 HOH HOH . F 4 HOH B 20 322 26 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 HMH . . . C 3 9.343 -22.194 10.517 0.7 38.12 ? CM2 HMH 301 A 1 HETATM 2 N N1A HMH . . . C 3 10.216 -21.796 8.211 0.7 75.09 ? N1A HMH 301 A 1 HETATM 3 C C2A HMH . . . C 3 9.842 -22.686 9.174 0.7 57.38 ? C2A HMH 301 A 1 HETATM 4 N N3A HMH . . . C 3 9.916 -24.017 8.916 0.7 70.18 ? N3A HMH 301 A 1 HETATM 5 C C4A HMH . . . C 3 10.36 -24.475 7.714 0.7 60.32 ? C4A HMH 301 A 1 HETATM 6 N N4A HMH . . . C 3 10.399 -25.822 7.557 0.7 56.96 ? N4A HMH 301 A 1 HETATM 7 C C5A HMH . . . C 3 10.744 -23.554 6.715 0.7 58.34 ? C5A HMH 301 A 1 HETATM 8 C C6A HMH . . . C 3 10.66 -22.198 7 0.7 60.96 ? C6A HMH 301 A 1 HETATM 9 C C7A HMH . A . C 3 11.248 -23.983 5.347 0.35 71.06 ? C7A HMH 301 A 1 HETATM 10 C C7A HMH . B . C 3 11.244 -23.953 5.345 0.35 64.99 ? C7A HMH 301 A 1 HETATM 11 O O1 HMH . A . C 3 10.828 -25.305 5.008 0.35 70.04 ? O1 HMH 301 A 1 HETATM 12 O O1 HMH . B . C 3 10.815 -22.973 4.407 0.35 52.24 ? O1 HMH 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 12 #