data_5ZIM # _model_server_result.job_id 5rvBiRqAUVnGozEVQzQmgA _model_server_result.datetime_utc '2024-11-26 16:59:10' _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 5zim # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 5ZIM # _exptl.entry_id 5ZIM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DI-PHYTANYL-GLYCEROL _entity.pdbx_number_of_molecules 4 _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 5ZIM _cell.length_a 60.6 _cell.length_b 60.6 _cell.length_c 110.71 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZIM _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_635 -y+1,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.2 -104.962279 0 3 'crystal symmetry operation' 3_865 -x+y+3,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 151.5 52.481139 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 ? 3 E N N ? 3 F N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 212 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 250 _struct_conn.ptnr2_symmetry 1_555 _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 1.35 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C43 H88 O3' _chem_comp.formula_weight 653.157 _chem_comp.id L2P _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DI-PHYTANYL-GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL # 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 L2P sing 139 n n C1 C2 L2P sing 140 n n C1 H12 L2P sing 141 n n C1 H11 L2P sing 142 n n O1 C11 L2P sing 143 n n C2 O2 L2P sing 144 n n C2 C3 L2P sing 145 n n C2 H2 L2P sing 146 n n O2 C41 L2P sing 147 n n C3 O3 L2P sing 148 n n C3 H32 L2P sing 149 n n C3 H31 L2P sing 150 n n O3 H3O L2P sing 151 n n C11 C12 L2P sing 152 n n C11 H112 L2P sing 153 n n C11 H111 L2P sing 154 n n C12 C13 L2P sing 155 n n C12 H122 L2P sing 156 n n C12 H121 L2P sing 157 n n C13 C14 L2P sing 158 n n C13 C15 L2P sing 159 n n C13 H13 L2P sing 160 n n C14 H143 L2P sing 161 n n C14 H142 L2P sing 162 n n C14 H141 L2P sing 163 n n C15 C16 L2P sing 164 n n C15 H152 L2P sing 165 n n C15 H151 L2P sing 166 n n C16 C17 L2P sing 167 n n C16 H162 L2P sing 168 n n C16 H161 L2P sing 169 n n C17 C18 L2P sing 170 n n C17 H172 L2P sing 171 n n C17 H171 L2P sing 172 n n C18 C19 L2P sing 173 n n C18 C20 L2P sing 174 n n C18 H18 L2P sing 175 n n C19 H193 L2P sing 176 n n C19 H192 L2P sing 177 n n C19 H191 L2P sing 178 n n C20 C21 L2P sing 179 n n C20 H202 L2P sing 180 n n C20 H201 L2P sing 181 n n C21 C22 L2P sing 182 n n C21 H212 L2P sing 183 n n C21 H211 L2P sing 184 n n C22 C23 L2P sing 185 n n C22 H222 L2P sing 186 n n C22 H221 L2P sing 187 n n C23 C24 L2P sing 188 n n C23 C25 L2P sing 189 n n C23 H23 L2P sing 190 n n C24 H243 L2P sing 191 n n C24 H242 L2P sing 192 n n C24 H241 L2P sing 193 n n C25 C26 L2P sing 194 n n C25 H252 L2P sing 195 n n C25 H251 L2P sing 196 n n C26 C27 L2P sing 197 n n C26 H262 L2P sing 198 n n C26 H261 L2P sing 199 n n C27 C28 L2P sing 200 n n C27 H272 L2P sing 201 n n C27 H271 L2P sing 202 n n C28 C29 L2P sing 203 n n C28 C30 L2P sing 204 n n C28 H28 L2P sing 205 n n C29 H293 L2P sing 206 n n C29 H292 L2P sing 207 n n C29 H291 L2P sing 208 n n C30 H303 L2P sing 209 n n C30 H302 L2P sing 210 n n C30 H301 L2P sing 211 n n C41 C42 L2P sing 212 n n C41 H412 L2P sing 213 n n C41 H411 L2P sing 214 n n C42 C43 L2P sing 215 n n C42 H422 L2P sing 216 n n C42 H421 L2P sing 217 n n C43 C44 L2P sing 218 n n C43 C45 L2P sing 219 n n C43 H43 L2P sing 220 n n C44 H443 L2P sing 221 n n C44 H442 L2P sing 222 n n C44 H441 L2P sing 223 n n C45 C46 L2P sing 224 n n C45 H452 L2P sing 225 n n C45 H451 L2P sing 226 n n C46 C47 L2P sing 227 n n C46 H462 L2P sing 228 n n C46 H461 L2P sing 229 n n C47 C48 L2P sing 230 n n C47 H472 L2P sing 231 n n C47 H471 L2P sing 232 n n C48 C49 L2P sing 233 n n C48 C50 L2P sing 234 n n C48 H48 L2P sing 235 n n C49 H493 L2P sing 236 n n C49 H492 L2P sing 237 n n C49 H491 L2P sing 238 n n C50 C51 L2P sing 239 n n C50 H502 L2P sing 240 n n C50 H501 L2P sing 241 n n C51 C52 L2P sing 242 n n C51 H512 L2P sing 243 n n C51 H511 L2P sing 244 n n C52 C53 L2P sing 245 n n C52 H522 L2P sing 246 n n C52 H521 L2P sing 247 n n C53 C54 L2P sing 248 n n C53 C55 L2P sing 249 n n C53 H53 L2P sing 250 n n C54 H543 L2P sing 251 n n C54 H542 L2P sing 252 n n C54 H541 L2P sing 253 n n C55 C56 L2P sing 254 n n C55 H552 L2P sing 255 n n C55 H551 L2P sing 256 n n C56 C57 L2P sing 257 n n C56 H562 L2P sing 258 n n C56 H561 L2P sing 259 n n C57 C58 L2P sing 260 n n C57 H572 L2P sing 261 n n C57 H571 L2P sing 262 n n C58 C59 L2P sing 263 n n C58 C60 L2P sing 264 n n C58 H58 L2P sing 265 n n C59 H593 L2P sing 266 n n C59 H592 L2P sing 267 n n C59 H591 L2P sing 268 n n C60 H603 L2P sing 269 n n C60 H602 L2P sing 270 n n C60 H601 L2P sing 271 n n # _atom_sites.entry_id 5ZIM _atom_sites.fract_transf_matrix[1][1] 0.016502 _atom_sites.fract_transf_matrix[1][2] 0.009527 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019054 _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] 0.009033 _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 RET A 1 250 250 RET RET . C 3 L2P A 1 270 270 L2P L2P . D 3 L2P A 1 290 290 L2P L2P . E 3 L2P A 1 300 300 L2P L2P . F 3 L2P A 1 310 310 L2P L2P . G 4 HOH A 1 402 402 HOH HOH . G 4 HOH A 2 401 401 HOH HOH . G 4 HOH A 3 406 406 HOH HOH . G 4 HOH A 4 513 513 HOH HOH . G 4 HOH A 5 512 512 HOH HOH . G 4 HOH A 6 502 502 HOH HOH . G 4 HOH A 7 514 514 HOH HOH . G 4 HOH A 8 403 403 HOH HOH . G 4 HOH A 9 404 404 HOH HOH . G 4 HOH A 10 415 415 HOH HOH . G 4 HOH A 11 420 420 HOH HOH . G 4 HOH A 12 411 411 HOH HOH . G 4 HOH A 13 412 412 HOH HOH . G 4 HOH A 14 501 501 HOH HOH . G 4 HOH A 15 407 407 HOH HOH . G 4 HOH A 16 511 511 HOH HOH . G 4 HOH A 17 405 405 HOH HOH . G 4 HOH A 18 419 419 HOH HOH . G 4 HOH A 19 416 416 HOH HOH . G 4 HOH A 20 450 450 HOH HOH . G 4 HOH A 21 451 451 HOH HOH . G 4 HOH A 22 452 452 HOH HOH . G 4 HOH A 23 453 453 HOH HOH . G 4 HOH A 24 454 454 HOH HOH . G 4 HOH A 25 455 455 HOH HOH . G 4 HOH A 26 456 456 HOH HOH . G 4 HOH A 27 457 457 HOH HOH . G 4 HOH A 28 458 458 HOH HOH . G 4 HOH A 29 459 459 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 L2P . . . E 3 63.245 -4.26 -41.777 1 64.07 ? C1 L2P 300 A 1 HETATM 2 O O1 L2P . . . E 3 64.282 -3.945 -40.823 1 63.37 ? O1 L2P 300 A 1 HETATM 3 C C2 L2P . . . E 3 61.838 -4.413 -41.17 1 65.43 ? C2 L2P 300 A 1 HETATM 4 O O2 L2P . . . E 3 61.993 -5.505 -40.242 1 67.78 ? O2 L2P 300 A 1 HETATM 5 C C3 L2P . . . E 3 60.728 -4.623 -42.211 1 64.98 ? C3 L2P 300 A 1 HETATM 6 O O3 L2P . . . E 3 60.796 -3.755 -43.367 1 62.65 ? O3 L2P 300 A 1 HETATM 7 C C11 L2P . . . E 3 64.186 -2.735 -40.044 1 63.3 ? C11 L2P 300 A 1 HETATM 8 C C12 L2P . . . E 3 63.305 -2.844 -38.783 1 63.27 ? C12 L2P 300 A 1 HETATM 9 C C13 L2P . . . E 3 63.79 -1.967 -37.616 1 62.62 ? C13 L2P 300 A 1 HETATM 10 C C14 L2P . . . E 3 65.325 -2.004 -37.433 1 62.15 ? C14 L2P 300 A 1 HETATM 11 C C15 L2P . . . E 3 63.045 -2.232 -36.288 1 61.56 ? C15 L2P 300 A 1 HETATM 12 C C16 L2P . . . E 3 63.862 -1.771 -35.072 1 62.5 ? C16 L2P 300 A 1 HETATM 13 C C17 L2P . . . E 3 64.418 -2.916 -34.224 1 62.14 ? C17 L2P 300 A 1 HETATM 14 C C18 L2P . . . E 3 63.98 -2.817 -32.744 1 62.35 ? C18 L2P 300 A 1 HETATM 15 C C19 L2P . . . E 3 62.441 -2.706 -32.587 1 62.22 ? C19 L2P 300 A 1 HETATM 16 C C20 L2P . . . E 3 64.737 -1.716 -31.981 1 63.22 ? C20 L2P 300 A 1 HETATM 17 C C21 L2P . . . E 3 64.969 -2.057 -30.504 1 64.29 ? C21 L2P 300 A 1 HETATM 18 C C22 L2P . . . E 3 65.974 -1.13 -29.815 1 64.25 ? C22 L2P 300 A 1 HETATM 19 C C23 L2P . . . E 3 65.653 -0.807 -28.362 1 63.81 ? C23 L2P 300 A 1 HETATM 20 C C24 L2P . . . E 3 64.202 -0.414 -28.091 1 62.26 ? C24 L2P 300 A 1 HETATM 21 C C25 L2P . . . E 3 66.737 -0.023 -27.624 1 64.13 ? C25 L2P 300 A 1 HETATM 22 C C26 L2P . . . E 3 68.183 -0.678 -27.845 1 63.85 ? C26 L2P 300 A 1 HETATM 23 C C27 L2P . . . E 3 69.268 0.071 -27.051 1 62.27 ? C27 L2P 300 A 1 HETATM 24 C C28 L2P . . . E 3 69.361 -0.368 -25.57 1 62.47 ? C28 L2P 300 A 1 HETATM 25 C C29 L2P . . . E 3 67.998 -0.529 -24.881 1 64 ? C29 L2P 300 A 1 HETATM 26 C C30 L2P . . . E 3 70.327 -1.571 -25.36 1 62.33 ? C30 L2P 300 A 1 HETATM 27 C C41 L2P . . . E 3 60.865 -5.87 -39.413 1 66.76 ? C41 L2P 300 A 1 HETATM 28 C C42 L2P . . . E 3 60.743 -5.038 -38.131 1 67.18 ? C42 L2P 300 A 1 HETATM 29 C C43 L2P . . . E 3 60.342 -5.887 -36.923 1 67.41 ? C43 L2P 300 A 1 HETATM 30 C C44 L2P . . . E 3 59.235 -6.927 -37.254 1 71.76 ? C44 L2P 300 A 1 HETATM 31 C C45 L2P . . . E 3 60.02 -5.028 -35.697 1 67.98 ? C45 L2P 300 A 1 HETATM 32 C C46 L2P . . . E 3 60.088 -5.826 -34.393 1 68.21 ? C46 L2P 300 A 1 HETATM 33 C C47 L2P . . . E 3 60.116 -4.943 -33.147 1 68.63 ? C47 L2P 300 A 1 HETATM 34 C C48 L2P . . . E 3 59.753 -5.709 -31.874 1 69.52 ? C48 L2P 300 A 1 HETATM 35 C C49 L2P . . . E 3 58.238 -5.972 -31.732 1 67.3 ? C49 L2P 300 A 1 HETATM 36 C C50 L2P . . . E 3 60.404 -5.115 -30.629 1 70.08 ? C50 L2P 300 A 1 HETATM 37 C C51 L2P . . . E 3 60.499 -6.105 -29.466 1 70.39 ? C51 L2P 300 A 1 HETATM 38 C C52 L2P . . . E 3 60.316 -5.402 -28.072 1 71.28 ? C52 L2P 300 A 1 HETATM 39 C C53 L2P . . . E 3 60.483 -6.5 -26.934 1 71.28 ? C53 L2P 300 A 1 HETATM 40 C C54 L2P . . . E 3 60.015 -7.933 -27.339 1 72.56 ? C54 L2P 300 A 1 HETATM 41 C C55 L2P . . . E 3 59.916 -5.997 -25.601 1 71.99 ? C55 L2P 300 A 1 HETATM 42 C C56 L2P . . . E 3 59.817 -4.398 -25.594 1 70.8 ? C56 L2P 300 A 1 HETATM 43 C C57 L2P . . . E 3 59.196 -3.903 -24.282 1 68.73 ? C57 L2P 300 A 1 HETATM 44 C C58 L2P . . . E 3 60.075 -2.91 -23.516 1 65.15 ? C58 L2P 300 A 1 HETATM 45 C C59 L2P . . . E 3 59.433 -1.519 -23.378 1 63.78 ? C59 L2P 300 A 1 HETATM 46 C C60 L2P . . . E 3 60.61 -3.454 -22.186 1 59.62 ? C60 L2P 300 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #