data_3RO7 # _model_server_result.job_id 3n_mVKOFh_qMyH1oxR5nHw _model_server_result.datetime_utc '2024-11-14 17:52:07' _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 3ro7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3RO7 # _exptl.entry_id 3RO7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 126.113 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMINE _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 3RO7 _cell.length_a 126.291 _cell.length_b 126.291 _cell.length_c 109.472 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RO7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1,2 A,B,C,D 2 1,3 A,B,C,D 3 1,4,5,3,6,7 # 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' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 72.914143 72.981333 3 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 109.472 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 109.472 7 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 109.472 # _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 C LEU 54 A LEU 53 1_555 A N MSE 55 A MSE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale2 A C MSE 55 A MSE 54 1_555 A N GLU 56 A GLU 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale3 A C SER 74 A SER 73 1_555 A N MSE 75 A MSE 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 75 A MSE 74 1_555 A N SER 76 A SER 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A C LYS 131 A LYS 130 1_555 A N MSE 132 A MSE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C MSE 132 A MSE 131 1_555 A N ASP 133 A ASP 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale7 A C GLU 139 A GLU 138 1_555 A N MSE 140 A MSE 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale8 A C MSE 140 A MSE 139 1_555 A N PRO 141 A PRO 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale9 A C PRO 144 A PRO 143 1_555 A N MSE 145 A MSE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale10 A C MSE 145 A MSE 144 1_555 A N MSE 146 A MSE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale11 A C MSE 146 A MSE 145 1_555 A N VAL 147 A VAL 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _chem_comp.formula 'C5 H6 N2 O2' _chem_comp.formula_weight 126.113 _chem_comp.id TDR _chem_comp.mon_nstd_flag . _chem_comp.name THYMINE _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 TDR sing 294 n n N1 C6 TDR sing 295 n n N1 HN1 TDR sing 296 n n C2 O2 TDR doub 297 n n C2 N3 TDR sing 298 n n N3 C4 TDR sing 299 n n N3 HN3 TDR sing 300 n n C4 O4 TDR doub 301 n n C4 C5 TDR sing 302 n n C5 CM5 TDR sing 303 n n C5 C6 TDR doub 304 n n CM5 H5M1 TDR sing 305 n n CM5 H5M2 TDR sing 306 n n CM5 H5M3 TDR sing 307 n n C6 H6 TDR sing 308 n n # _atom_sites.entry_id 3RO7 _atom_sites.fract_transf_matrix[1][1] 0.007918 _atom_sites.fract_transf_matrix[1][2] 0.004572 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009143 _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] 0.009135 _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 TDR A 1 300 300 TDR TDR . C 3 SO4 A 1 301 301 SO4 SO4 . D 4 HOH A 1 265 1 HOH HOH . D 4 HOH A 2 266 2 HOH HOH . D 4 HOH A 3 267 3 HOH HOH . D 4 HOH A 4 268 4 HOH HOH . D 4 HOH A 5 269 5 HOH HOH . D 4 HOH A 6 270 6 HOH HOH . D 4 HOH A 7 271 7 HOH HOH . D 4 HOH A 8 272 8 HOH HOH . D 4 HOH A 9 273 9 HOH HOH . D 4 HOH A 10 274 10 HOH HOH . D 4 HOH A 11 275 11 HOH HOH . D 4 HOH A 12 276 12 HOH HOH . D 4 HOH A 13 277 13 HOH HOH . D 4 HOH A 14 278 14 HOH HOH . D 4 HOH A 15 279 15 HOH HOH . D 4 HOH A 16 280 16 HOH HOH . D 4 HOH A 17 281 17 HOH HOH . D 4 HOH A 18 282 18 HOH HOH . D 4 HOH A 19 283 19 HOH HOH . D 4 HOH A 20 284 20 HOH HOH . D 4 HOH A 21 285 21 HOH HOH . D 4 HOH A 22 286 22 HOH HOH . D 4 HOH A 23 287 23 HOH HOH . D 4 HOH A 24 288 24 HOH HOH . D 4 HOH A 25 289 25 HOH HOH . D 4 HOH A 26 290 26 HOH HOH . D 4 HOH A 27 291 27 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 N N1 TDR . . . B 2 11.676 26.426 27.26 1 61.06 ? N1 TDR 300 A 1 HETATM 2 C C2 TDR . . . B 2 11.008 25.329 27.658 1 60.38 ? C2 TDR 300 A 1 HETATM 3 O O2 TDR . . . B 2 10.956 25.028 28.855 1 57.82 ? O2 TDR 300 A 1 HETATM 4 N N3 TDR . . . B 2 10.378 24.526 26.782 1 62.31 ? N3 TDR 300 A 1 HETATM 5 C C4 TDR . . . B 2 10.392 24.774 25.457 1 61.93 ? C4 TDR 300 A 1 HETATM 6 O O4 TDR . . . B 2 9.795 24.004 24.668 1 61.76 ? O4 TDR 300 A 1 HETATM 7 C C5 TDR . . . B 2 11.127 25.98 24.962 1 62.69 ? C5 TDR 300 A 1 HETATM 8 C CM5 TDR . . . B 2 11.183 26.313 23.479 1 60.28 ? CM5 TDR 300 A 1 HETATM 9 C C6 TDR . . . B 2 11.758 26.764 25.942 1 62.05 ? C6 TDR 300 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #