data_2RDM # _model_server_result.job_id JRCMUoi97zpwC3cruC3VVA _model_server_result.datetime_utc '2025-08-31 21:51:02' _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 2rdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":132}' # _entry.id 2RDM # _exptl.entry_id 2RDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.96 _cell.angle_gamma 90 _cell.entry_id 2RDM _cell.length_a 122.593 _cell.length_b 58.657 _cell.length_c 60.301 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 hexameric 6 software_defined_assembly 1 PISA trimeric 3 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,G,H,I 1 1,2 A,D,E,G 2 2 B,C,F,H,I 2 1 # 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' 2_555 -x,y,-z -1 0 0 0 1 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 ? 2 D N N ? 2 E N N ? 2 F 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 GLU 43 A GLU 41 1_555 A N MSE 44 A MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale2 A C MSE 44 A MSE 42 1_555 A N LEU 45 A LEU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale3 A C ASN 79 A ASN 77 1_555 A N MSE 80 A MSE 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C MSE 80 A MSE 78 1_555 A N PRO 81 A PRO 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale5 B C GLU 43 B GLU 41 1_555 B N MSE 44 B MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 B C MSE 44 B MSE 42 1_555 B N LEU 45 B LEU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 B C ASN 79 B ASN 77 1_555 B N MSE 80 B MSE 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale8 B C MSE 80 B MSE 78 1_555 B N PRO 81 B PRO 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale9 C C GLU 43 C GLU 41 1_555 C N MSE 44 C MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 C C MSE 44 C MSE 42 1_555 C N LEU 45 C LEU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale11 C C ASN 79 C ASN 77 1_555 C N MSE 80 C MSE 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale12 C C MSE 80 C MSE 78 1_555 C N PRO 81 C PRO 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 2RDM _atom_sites.fract_transf_matrix[1][1] 0.008157 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00433 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017048 _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] 0.018776 _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 D 2 GOL A 1 131 1 GOL GOL . E 2 GOL A 1 132 1 GOL GOL . F 2 GOL C 1 131 1 GOL GOL . G 3 HOH A 1 133 1 HOH HOH . G 3 HOH A 2 134 9 HOH HOH . G 3 HOH A 3 135 10 HOH HOH . G 3 HOH A 4 136 27 HOH HOH . G 3 HOH A 5 137 39 HOH HOH . G 3 HOH A 6 138 50 HOH HOH . G 3 HOH A 7 139 56 HOH HOH . G 3 HOH A 8 140 57 HOH HOH . G 3 HOH A 9 141 66 HOH HOH . G 3 HOH A 10 142 69 HOH HOH . G 3 HOH A 11 143 71 HOH HOH . G 3 HOH A 12 144 74 HOH HOH . G 3 HOH A 13 145 83 HOH HOH . G 3 HOH A 14 146 87 HOH HOH . G 3 HOH A 15 147 92 HOH HOH . G 3 HOH A 16 148 94 HOH HOH . G 3 HOH A 17 149 113 HOH HOH . G 3 HOH A 18 150 117 HOH HOH . G 3 HOH A 19 151 127 HOH HOH . G 3 HOH A 20 152 128 HOH HOH . G 3 HOH A 21 153 129 HOH HOH . G 3 HOH A 22 154 131 HOH HOH . G 3 HOH A 23 155 135 HOH HOH . G 3 HOH A 24 156 140 HOH HOH . G 3 HOH A 25 157 143 HOH HOH . G 3 HOH A 26 158 145 HOH HOH . G 3 HOH A 27 159 147 HOH HOH . G 3 HOH A 28 160 154 HOH HOH . G 3 HOH A 29 161 165 HOH HOH . G 3 HOH A 30 162 168 HOH HOH . G 3 HOH A 31 163 176 HOH HOH . G 3 HOH A 32 164 180 HOH HOH . G 3 HOH A 33 165 184 HOH HOH . G 3 HOH A 34 166 186 HOH HOH . G 3 HOH A 35 167 187 HOH HOH . G 3 HOH A 36 168 200 HOH HOH . G 3 HOH A 37 169 214 HOH HOH . G 3 HOH A 38 170 215 HOH HOH . G 3 HOH A 39 171 216 HOH HOH . G 3 HOH A 40 172 217 HOH HOH . G 3 HOH A 41 173 218 HOH HOH . G 3 HOH A 42 174 219 HOH HOH . G 3 HOH A 43 175 220 HOH HOH . G 3 HOH A 44 176 221 HOH HOH . G 3 HOH A 45 177 222 HOH HOH . G 3 HOH A 46 178 223 HOH HOH . G 3 HOH A 47 179 224 HOH HOH . G 3 HOH A 48 180 225 HOH HOH . G 3 HOH A 49 181 226 HOH HOH . G 3 HOH A 50 182 228 HOH HOH . G 3 HOH A 51 183 229 HOH HOH . G 3 HOH A 52 184 230 HOH HOH . G 3 HOH A 53 185 231 HOH HOH . G 3 HOH A 54 186 263 HOH HOH . G 3 HOH A 55 187 264 HOH HOH . G 3 HOH A 56 188 265 HOH HOH . G 3 HOH A 57 189 266 HOH HOH . G 3 HOH A 58 190 277 HOH HOH . G 3 HOH A 59 191 281 HOH HOH . G 3 HOH A 60 192 282 HOH HOH . G 3 HOH A 61 193 284 HOH HOH . G 3 HOH A 62 194 285 HOH HOH . G 3 HOH A 63 195 286 HOH HOH . G 3 HOH A 64 196 287 HOH HOH . G 3 HOH A 65 197 288 HOH HOH . G 3 HOH A 66 198 289 HOH HOH . G 3 HOH A 67 199 298 HOH HOH . H 3 HOH B 1 131 7 HOH HOH . H 3 HOH B 2 132 12 HOH HOH . H 3 HOH B 3 133 13 HOH HOH . H 3 HOH B 4 134 19 HOH HOH . H 3 HOH B 5 135 23 HOH HOH . H 3 HOH B 6 136 24 HOH HOH . H 3 HOH B 7 137 25 HOH HOH . H 3 HOH B 8 138 29 HOH HOH . H 3 HOH B 9 139 31 HOH HOH . H 3 HOH B 10 140 33 HOH HOH . H 3 HOH B 11 141 42 HOH HOH . H 3 HOH B 12 142 45 HOH HOH . H 3 HOH B 13 143 47 HOH HOH . H 3 HOH B 14 144 51 HOH HOH . H 3 HOH B 15 145 59 HOH HOH . H 3 HOH B 16 146 62 HOH HOH . H 3 HOH B 17 147 63 HOH HOH . H 3 HOH B 18 148 64 HOH HOH . H 3 HOH B 19 149 65 HOH HOH . H 3 HOH B 20 150 68 HOH HOH . H 3 HOH B 21 151 72 HOH HOH . H 3 HOH B 22 152 77 HOH HOH . H 3 HOH B 23 153 78 HOH HOH . H 3 HOH B 24 154 80 HOH HOH . H 3 HOH B 25 155 86 HOH HOH . H 3 HOH B 26 156 93 HOH HOH . H 3 HOH B 27 157 100 HOH HOH . H 3 HOH B 28 158 102 HOH HOH . H 3 HOH B 29 159 108 HOH HOH . H 3 HOH B 30 160 111 HOH HOH . H 3 HOH B 31 161 114 HOH HOH . H 3 HOH B 32 162 120 HOH HOH . H 3 HOH B 33 163 124 HOH HOH . H 3 HOH B 34 164 130 HOH HOH . H 3 HOH B 35 165 132 HOH HOH . H 3 HOH B 36 166 139 HOH HOH . H 3 HOH B 37 167 148 HOH HOH . H 3 HOH B 38 168 149 HOH HOH . H 3 HOH B 39 169 153 HOH HOH . H 3 HOH B 40 170 167 HOH HOH . H 3 HOH B 41 171 171 HOH HOH . H 3 HOH B 42 172 174 HOH HOH . H 3 HOH B 43 173 175 HOH HOH . H 3 HOH B 44 174 194 HOH HOH . H 3 HOH B 45 175 202 HOH HOH . H 3 HOH B 46 176 203 HOH HOH . H 3 HOH B 47 177 205 HOH HOH . H 3 HOH B 48 178 206 HOH HOH . H 3 HOH B 49 179 213 HOH HOH . H 3 HOH B 50 180 227 HOH HOH . H 3 HOH B 51 181 232 HOH HOH . H 3 HOH B 52 182 233 HOH HOH . H 3 HOH B 53 183 235 HOH HOH . H 3 HOH B 54 184 236 HOH HOH . H 3 HOH B 55 185 237 HOH HOH . H 3 HOH B 56 186 238 HOH HOH . H 3 HOH B 57 187 239 HOH HOH . H 3 HOH B 58 188 240 HOH HOH . H 3 HOH B 59 189 241 HOH HOH . H 3 HOH B 60 190 242 HOH HOH . H 3 HOH B 61 191 243 HOH HOH . H 3 HOH B 62 192 268 HOH HOH . H 3 HOH B 63 193 269 HOH HOH . H 3 HOH B 64 194 270 HOH HOH . H 3 HOH B 65 195 276 HOH HOH . H 3 HOH B 66 196 279 HOH HOH . H 3 HOH B 67 197 290 HOH HOH . H 3 HOH B 68 198 291 HOH HOH . H 3 HOH B 69 199 292 HOH HOH . H 3 HOH B 70 200 293 HOH HOH . I 3 HOH C 1 132 2 HOH HOH . I 3 HOH C 2 133 8 HOH HOH . I 3 HOH C 3 134 11 HOH HOH . I 3 HOH C 4 135 15 HOH HOH . I 3 HOH C 5 136 28 HOH HOH . I 3 HOH C 6 137 37 HOH HOH . I 3 HOH C 7 138 38 HOH HOH . I 3 HOH C 8 139 40 HOH HOH . I 3 HOH C 9 140 43 HOH HOH . I 3 HOH C 10 141 54 HOH HOH . I 3 HOH C 11 142 55 HOH HOH . I 3 HOH C 12 143 60 HOH HOH . I 3 HOH C 13 144 61 HOH HOH . I 3 HOH C 14 145 70 HOH HOH . I 3 HOH C 15 146 73 HOH HOH . I 3 HOH C 16 147 79 HOH HOH . I 3 HOH C 17 148 90 HOH HOH . I 3 HOH C 18 149 109 HOH HOH . I 3 HOH C 19 150 115 HOH HOH . I 3 HOH C 20 151 118 HOH HOH . I 3 HOH C 21 152 123 HOH HOH . I 3 HOH C 22 153 137 HOH HOH . I 3 HOH C 23 154 138 HOH HOH . I 3 HOH C 24 155 142 HOH HOH . I 3 HOH C 25 156 156 HOH HOH . I 3 HOH C 26 157 173 HOH HOH . I 3 HOH C 27 158 182 HOH HOH . I 3 HOH C 28 159 185 HOH HOH . I 3 HOH C 29 160 192 HOH HOH . I 3 HOH C 30 161 196 HOH HOH . I 3 HOH C 31 162 210 HOH HOH . I 3 HOH C 32 163 212 HOH HOH . I 3 HOH C 33 164 244 HOH HOH . I 3 HOH C 34 165 245 HOH HOH . I 3 HOH C 35 166 246 HOH HOH . I 3 HOH C 36 167 247 HOH HOH . I 3 HOH C 37 168 248 HOH HOH . I 3 HOH C 38 169 249 HOH HOH . I 3 HOH C 39 170 250 HOH HOH . I 3 HOH C 40 171 251 HOH HOH . I 3 HOH C 41 172 252 HOH HOH . I 3 HOH C 42 173 253 HOH HOH . I 3 HOH C 43 174 254 HOH HOH . I 3 HOH C 44 175 255 HOH HOH . I 3 HOH C 45 176 256 HOH HOH . I 3 HOH C 46 177 258 HOH HOH . I 3 HOH C 47 178 259 HOH HOH . I 3 HOH C 48 179 260 HOH HOH . I 3 HOH C 49 180 261 HOH HOH . I 3 HOH C 50 181 262 HOH HOH . I 3 HOH C 51 182 271 HOH HOH . I 3 HOH C 52 183 272 HOH HOH . I 3 HOH C 53 184 273 HOH HOH . I 3 HOH C 54 185 274 HOH HOH . I 3 HOH C 55 186 278 HOH HOH . I 3 HOH C 56 187 280 HOH HOH . I 3 HOH C 57 188 294 HOH HOH . I 3 HOH C 58 189 295 HOH HOH . I 3 HOH C 59 190 296 HOH HOH . I 3 HOH C 60 191 297 HOH HOH . I 3 HOH C 61 192 299 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 C1 GOL . . . E 2 -3.425 58.779 14.193 1 70.48 ? C1 GOL 132 A 1 HETATM 2 O O1 GOL . . . E 2 -4.282 59.744 14.763 1 72.14 ? O1 GOL 132 A 1 HETATM 3 C C2 GOL . . . E 2 -2.325 59.494 13.421 1 73.1 ? C2 GOL 132 A 1 HETATM 4 O O2 GOL . . . E 2 -2.673 59.566 12.054 1 77.85 ? O2 GOL 132 A 1 HETATM 5 C C3 GOL . . . E 2 -1.028 58.716 13.574 1 68.33 ? C3 GOL 132 A 1 HETATM 6 O O3 GOL . . . E 2 0.009 59.462 12.983 1 58.03 ? O3 GOL 132 A 1 # _model_server_stats.io_time_ms 292 _model_server_stats.parse_time_ms 115 _model_server_stats.create_model_time_ms 91 _model_server_stats.query_time_ms 638 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #