data_3RDQ # _model_server_result.job_id yuwPtEasy-dgp_7bO2lcVQ _model_server_result.datetime_utc '2024-11-17 06:42:22' _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 3rdq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3RDQ # _exptl.entry_id 3RDQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 214.262 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID' _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 90 _cell.entry_id 3RDQ _cell.length_a 57.275 _cell.length_b 57.275 _cell.length_c 183.742 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RDQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 metalc ? metalc1 A O ALA 132 A ALA 119 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc2 A OG SER 135 A SER 122 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc3 G O HOH . A HOH 163 1_555 C NI NI . A NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc4 G O HOH . A HOH 189 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc5 G O HOH . A HOH 259 1_555 C NI NI . A NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc6 B OI2 DTB . A DTB 300 1_555 C NI NI . A NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc7 B OI1 DTB . A DTB 300 1_555 C NI NI . A NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? # _chem_comp.formula 'C10 H18 N2 O3' _chem_comp.formula_weight 214.262 _chem_comp.id DTB _chem_comp.mon_nstd_flag . _chem_comp.name '6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-DESTHIOBIOTIN # 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 CN O DTB doub 70 n n CN N2 DTB sing 71 n n CN N1 DTB sing 72 n n N2 CR DTB sing 73 n n N2 HN2 DTB sing 74 n n CR CS DTB sing 75 n n CR CE DTB sing 76 n n CR HCR DTB sing 77 n n CS N1 DTB sing 78 n n CS CT DTB sing 79 n n CS HCS DTB sing 80 n n N1 HN1 DTB sing 81 n n CT HCT1 DTB sing 82 n n CT HCT2 DTB sing 83 n n CT HCT3 DTB sing 84 n n CE CD DTB sing 85 n n CE HCE1 DTB sing 86 n n CE HCE2 DTB sing 87 n n CD CG DTB sing 88 n n CD HCD1 DTB sing 89 n n CD HCD2 DTB sing 90 n n CG CB DTB sing 91 n n CG HCG1 DTB sing 92 n n CG HCG2 DTB sing 93 n n CB CA DTB sing 94 n n CB HCB1 DTB sing 95 n n CB HCB2 DTB sing 96 n n CA C DTB sing 97 n n CA HCA1 DTB sing 98 n n CA HCA2 DTB sing 99 n n C OI1 DTB doub 100 n n C OI2 DTB sing 101 n n OI2 HOI2 DTB sing 102 n n # _atom_sites.entry_id 3RDQ _atom_sites.fract_transf_matrix[1][1] 0.01746 _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] 0.01746 _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] 0.005442 _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 DTB A 1 300 300 DTB DTB . C 3 NI A 1 301 301 NI NI . D 4 NA A 1 303 303 NA NA . E 5 GOL A 1 302 302 GOL GOL . F 5 GOL A 1 304 304 GOL GOL . G 6 HOH A 1 141 141 HOH HOH . G 6 HOH A 2 142 142 HOH HOH . G 6 HOH A 3 143 143 HOH HOH . G 6 HOH A 4 144 144 HOH HOH . G 6 HOH A 5 145 145 HOH HOH . G 6 HOH A 6 146 146 HOH HOH . G 6 HOH A 7 147 147 HOH HOH . G 6 HOH A 8 148 148 HOH HOH . G 6 HOH A 9 149 149 HOH HOH . G 6 HOH A 10 150 150 HOH HOH . G 6 HOH A 11 151 151 HOH HOH . G 6 HOH A 12 152 152 HOH HOH . G 6 HOH A 13 153 153 HOH HOH . G 6 HOH A 14 154 154 HOH HOH . G 6 HOH A 15 155 155 HOH HOH . G 6 HOH A 16 156 156 HOH HOH . G 6 HOH A 17 157 157 HOH HOH . G 6 HOH A 18 158 158 HOH HOH . G 6 HOH A 19 159 159 HOH HOH . G 6 HOH A 20 160 160 HOH HOH . G 6 HOH A 21 161 161 HOH HOH . G 6 HOH A 22 162 162 HOH HOH . G 6 HOH A 23 163 163 HOH HOH . G 6 HOH A 24 164 164 HOH HOH . G 6 HOH A 25 165 165 HOH HOH . G 6 HOH A 26 166 166 HOH HOH . G 6 HOH A 27 167 167 HOH HOH . G 6 HOH A 28 168 168 HOH HOH . G 6 HOH A 29 169 169 HOH HOH . G 6 HOH A 30 170 170 HOH HOH . G 6 HOH A 31 171 171 HOH HOH . G 6 HOH A 32 172 172 HOH HOH . G 6 HOH A 33 173 173 HOH HOH . G 6 HOH A 34 174 174 HOH HOH . G 6 HOH A 35 175 175 HOH HOH . G 6 HOH A 36 176 176 HOH HOH . G 6 HOH A 37 177 177 HOH HOH . G 6 HOH A 38 178 178 HOH HOH . G 6 HOH A 39 179 179 HOH HOH . G 6 HOH A 40 180 180 HOH HOH . G 6 HOH A 41 181 181 HOH HOH . G 6 HOH A 42 182 182 HOH HOH . G 6 HOH A 43 183 183 HOH HOH . G 6 HOH A 44 184 184 HOH HOH . G 6 HOH A 45 185 185 HOH HOH . G 6 HOH A 46 186 186 HOH HOH . G 6 HOH A 47 187 187 HOH HOH . G 6 HOH A 48 188 188 HOH HOH . G 6 HOH A 49 189 189 HOH HOH . G 6 HOH A 50 190 190 HOH HOH . G 6 HOH A 51 191 191 HOH HOH . G 6 HOH A 52 192 192 HOH HOH . G 6 HOH A 53 193 193 HOH HOH . G 6 HOH A 54 194 194 HOH HOH . G 6 HOH A 55 195 195 HOH HOH . G 6 HOH A 56 196 196 HOH HOH . G 6 HOH A 57 197 197 HOH HOH . G 6 HOH A 58 198 198 HOH HOH . G 6 HOH A 59 199 199 HOH HOH . G 6 HOH A 60 200 200 HOH HOH . G 6 HOH A 61 201 201 HOH HOH . G 6 HOH A 62 202 202 HOH HOH . G 6 HOH A 63 203 203 HOH HOH . G 6 HOH A 64 204 204 HOH HOH . G 6 HOH A 65 205 205 HOH HOH . G 6 HOH A 66 206 206 HOH HOH . G 6 HOH A 67 207 207 HOH HOH . G 6 HOH A 68 208 208 HOH HOH . G 6 HOH A 69 209 209 HOH HOH . G 6 HOH A 70 210 210 HOH HOH . G 6 HOH A 71 211 211 HOH HOH . G 6 HOH A 72 212 212 HOH HOH . G 6 HOH A 73 213 213 HOH HOH . G 6 HOH A 74 214 214 HOH HOH . G 6 HOH A 75 215 215 HOH HOH . G 6 HOH A 76 216 216 HOH HOH . G 6 HOH A 77 217 217 HOH HOH . G 6 HOH A 78 218 218 HOH HOH . G 6 HOH A 79 219 219 HOH HOH . G 6 HOH A 80 220 220 HOH HOH . G 6 HOH A 81 221 221 HOH HOH . G 6 HOH A 82 222 222 HOH HOH . G 6 HOH A 83 223 223 HOH HOH . G 6 HOH A 84 224 224 HOH HOH . G 6 HOH A 85 225 225 HOH HOH . G 6 HOH A 86 226 226 HOH HOH . G 6 HOH A 87 227 227 HOH HOH . G 6 HOH A 88 228 228 HOH HOH . G 6 HOH A 89 229 229 HOH HOH . G 6 HOH A 90 230 230 HOH HOH . G 6 HOH A 91 231 231 HOH HOH . G 6 HOH A 92 232 232 HOH HOH . G 6 HOH A 93 233 233 HOH HOH . G 6 HOH A 94 234 234 HOH HOH . G 6 HOH A 95 235 235 HOH HOH . G 6 HOH A 96 236 236 HOH HOH . G 6 HOH A 97 237 237 HOH HOH . G 6 HOH A 98 238 238 HOH HOH . G 6 HOH A 99 239 239 HOH HOH . G 6 HOH A 100 240 240 HOH HOH . G 6 HOH A 101 241 241 HOH HOH . G 6 HOH A 102 242 242 HOH HOH . G 6 HOH A 103 243 243 HOH HOH . G 6 HOH A 104 244 244 HOH HOH . G 6 HOH A 105 245 245 HOH HOH . G 6 HOH A 106 246 246 HOH HOH . G 6 HOH A 107 247 247 HOH HOH . G 6 HOH A 108 248 248 HOH HOH . G 6 HOH A 109 249 249 HOH HOH . G 6 HOH A 110 250 250 HOH HOH . G 6 HOH A 111 251 251 HOH HOH . G 6 HOH A 112 252 252 HOH HOH . G 6 HOH A 113 253 253 HOH HOH . G 6 HOH A 114 254 254 HOH HOH . G 6 HOH A 115 255 255 HOH HOH . G 6 HOH A 116 256 256 HOH HOH . G 6 HOH A 117 257 257 HOH HOH . G 6 HOH A 118 258 258 HOH HOH . G 6 HOH A 119 259 259 HOH HOH . G 6 HOH A 120 260 260 HOH HOH . G 6 HOH A 121 261 261 HOH HOH . G 6 HOH A 122 262 262 HOH HOH . G 6 HOH A 123 263 263 HOH HOH . G 6 HOH A 124 264 264 HOH HOH . G 6 HOH A 125 265 265 HOH HOH . G 6 HOH A 126 266 266 HOH HOH . G 6 HOH A 127 267 267 HOH HOH . G 6 HOH A 128 268 268 HOH HOH . G 6 HOH A 129 269 269 HOH HOH . G 6 HOH A 130 270 270 HOH HOH . G 6 HOH A 131 271 271 HOH HOH . G 6 HOH A 132 272 272 HOH HOH . G 6 HOH A 133 273 273 HOH HOH . G 6 HOH A 134 274 274 HOH HOH . G 6 HOH A 135 275 275 HOH HOH . G 6 HOH A 136 276 276 HOH HOH . G 6 HOH A 137 277 277 HOH HOH . G 6 HOH A 138 278 278 HOH HOH . G 6 HOH A 139 279 279 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 CN DTB . . . B 2 15.489 28.878 -8.545 1 17.9 ? CN DTB 300 A 1 HETATM 2 O O DTB . . . B 2 14.231 29.107 -8.263 1 17.4 ? O DTB 300 A 1 HETATM 3 N N2 DTB . . . B 2 15.92 28.342 -9.628 1 17.58 ? N2 DTB 300 A 1 HETATM 4 C CR DTB . . . B 2 17.393 28.473 -9.73 1 16.74 ? CR DTB 300 A 1 HETATM 5 C CS DTB . . . B 2 17.761 28.946 -8.301 1 16.29 ? CS DTB 300 A 1 HETATM 6 N N1 DTB . . . B 2 16.459 29.248 -7.717 1 18.47 ? N1 DTB 300 A 1 HETATM 7 C CT DTB . . . B 2 18.475 27.89 -7.48 1 17.4 ? CT DTB 300 A 1 HETATM 8 C CE DTB . . . B 2 17.933 27.107 -10.158 1 16.05 ? CE DTB 300 A 1 HETATM 9 C CD DTB . . . B 2 17.557 26.789 -11.612 1 17.17 ? CD DTB 300 A 1 HETATM 10 C CG DTB . . . B 2 18.329 25.581 -12.159 1 15.7 ? CG DTB 300 A 1 HETATM 11 C CB DTB . . . B 2 17.602 25.007 -13.387 1 18.42 ? CB DTB 300 A 1 HETATM 12 C CA DTB . . . B 2 18.439 23.893 -14.062 1 19.04 ? CA DTB 300 A 1 HETATM 13 C C DTB . . . B 2 19.753 24.41 -14.62 1 19.2 ? C DTB 300 A 1 HETATM 14 O OI1 DTB . . . B 2 20.82 23.792 -14.399 1 18.92 ? OI1 DTB 300 A 1 HETATM 15 O OI2 DTB . . . B 2 19.737 25.441 -15.361 1 20.22 ? OI2 DTB 300 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 15 #