data_3VI0 # _model_server_result.job_id -pMjUXrU9pnUAYWR8xQwVA _model_server_result.datetime_utc '2024-11-13 05:12:18' _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 3vi0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":303}' # _entry.id 3VI0 # _exptl.entry_id 3VI0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DI-PHYTANYL-GLYCEROL _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 3VI0 _cell.length_a 102.3 _cell.length_b 102.3 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VI0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _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 _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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.3 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.15 88.594399 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 SGA MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC ? 400 GLC 2 n B MAN 2 B 2 MAN ? 410 MAN 2 n B SGA 3 B 3 SGA ? 420 SGA # 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 NZ LYS 229 A LYS 216 1_555 C C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? covale ? covale2 E O3 L2P . A L2P 303 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 SGA . B SGA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 163 n n C1 C2 L2P sing 164 n n C1 H12 L2P sing 165 n n C1 H11 L2P sing 166 n n O1 C11 L2P sing 167 n n C2 O2 L2P sing 168 n n C2 C3 L2P sing 169 n n C2 H2 L2P sing 170 n n O2 C41 L2P sing 171 n n C3 O3 L2P sing 172 n n C3 H32 L2P sing 173 n n C3 H31 L2P sing 174 n n O3 H3O L2P sing 175 n n C11 C12 L2P sing 176 n n C11 H112 L2P sing 177 n n C11 H111 L2P sing 178 n n C12 C13 L2P sing 179 n n C12 H122 L2P sing 180 n n C12 H121 L2P sing 181 n n C13 C14 L2P sing 182 n n C13 C15 L2P sing 183 n n C13 H13 L2P sing 184 n n C14 H143 L2P sing 185 n n C14 H142 L2P sing 186 n n C14 H141 L2P sing 187 n n C15 C16 L2P sing 188 n n C15 H152 L2P sing 189 n n C15 H151 L2P sing 190 n n C16 C17 L2P sing 191 n n C16 H162 L2P sing 192 n n C16 H161 L2P sing 193 n n C17 C18 L2P sing 194 n n C17 H172 L2P sing 195 n n C17 H171 L2P sing 196 n n C18 C19 L2P sing 197 n n C18 C20 L2P sing 198 n n C18 H18 L2P sing 199 n n C19 H193 L2P sing 200 n n C19 H192 L2P sing 201 n n C19 H191 L2P sing 202 n n C20 C21 L2P sing 203 n n C20 H202 L2P sing 204 n n C20 H201 L2P sing 205 n n C21 C22 L2P sing 206 n n C21 H212 L2P sing 207 n n C21 H211 L2P sing 208 n n C22 C23 L2P sing 209 n n C22 H222 L2P sing 210 n n C22 H221 L2P sing 211 n n C23 C24 L2P sing 212 n n C23 C25 L2P sing 213 n n C23 H23 L2P sing 214 n n C24 H243 L2P sing 215 n n C24 H242 L2P sing 216 n n C24 H241 L2P sing 217 n n C25 C26 L2P sing 218 n n C25 H252 L2P sing 219 n n C25 H251 L2P sing 220 n n C26 C27 L2P sing 221 n n C26 H262 L2P sing 222 n n C26 H261 L2P sing 223 n n C27 C28 L2P sing 224 n n C27 H272 L2P sing 225 n n C27 H271 L2P sing 226 n n C28 C29 L2P sing 227 n n C28 C30 L2P sing 228 n n C28 H28 L2P sing 229 n n C29 H293 L2P sing 230 n n C29 H292 L2P sing 231 n n C29 H291 L2P sing 232 n n C30 H303 L2P sing 233 n n C30 H302 L2P sing 234 n n C30 H301 L2P sing 235 n n C41 C42 L2P sing 236 n n C41 H412 L2P sing 237 n n C41 H411 L2P sing 238 n n C42 C43 L2P sing 239 n n C42 H422 L2P sing 240 n n C42 H421 L2P sing 241 n n C43 C44 L2P sing 242 n n C43 C45 L2P sing 243 n n C43 H43 L2P sing 244 n n C44 H443 L2P sing 245 n n C44 H442 L2P sing 246 n n C44 H441 L2P sing 247 n n C45 C46 L2P sing 248 n n C45 H452 L2P sing 249 n n C45 H451 L2P sing 250 n n C46 C47 L2P sing 251 n n C46 H462 L2P sing 252 n n C46 H461 L2P sing 253 n n C47 C48 L2P sing 254 n n C47 H472 L2P sing 255 n n C47 H471 L2P sing 256 n n C48 C49 L2P sing 257 n n C48 C50 L2P sing 258 n n C48 H48 L2P sing 259 n n C49 H493 L2P sing 260 n n C49 H492 L2P sing 261 n n C49 H491 L2P sing 262 n n C50 C51 L2P sing 263 n n C50 H502 L2P sing 264 n n C50 H501 L2P sing 265 n n C51 C52 L2P sing 266 n n C51 H512 L2P sing 267 n n C51 H511 L2P sing 268 n n C52 C53 L2P sing 269 n n C52 H522 L2P sing 270 n n C52 H521 L2P sing 271 n n C53 C54 L2P sing 272 n n C53 C55 L2P sing 273 n n C53 H53 L2P sing 274 n n C54 H543 L2P sing 275 n n C54 H542 L2P sing 276 n n C54 H541 L2P sing 277 n n C55 C56 L2P sing 278 n n C55 H552 L2P sing 279 n n C55 H551 L2P sing 280 n n C56 C57 L2P sing 281 n n C56 H562 L2P sing 282 n n C56 H561 L2P sing 283 n n C57 C58 L2P sing 284 n n C57 H572 L2P sing 285 n n C57 H571 L2P sing 286 n n C58 C59 L2P sing 287 n n C58 C60 L2P sing 288 n n C58 H58 L2P sing 289 n n C59 H593 L2P sing 290 n n C59 H592 L2P sing 291 n n C59 H591 L2P sing 292 n n C60 H603 L2P sing 293 n n C60 H602 L2P sing 294 n n C60 H601 L2P sing 295 n n # _atom_sites.entry_id 3VI0 _atom_sites.fract_transf_matrix[1][1] 0.009775 _atom_sites.fract_transf_matrix[1][2] 0.005644 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011287 _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] 0.008905 _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 RET A 1 301 250 RET RET . D 4 SOG A 1 302 430 SOG SOG . E 5 L2P A 1 303 270 L2P L2P . F 6 HOH A 1 401 600 HOH HOH . F 6 HOH A 2 402 601 HOH HOH . F 6 HOH A 3 403 604 HOH HOH . F 6 HOH A 4 404 605 HOH HOH . F 6 HOH A 5 405 606 HOH HOH . F 6 HOH A 6 406 607 HOH HOH . F 6 HOH A 7 407 608 HOH HOH . F 6 HOH A 8 408 609 HOH HOH . F 6 HOH A 9 409 610 HOH HOH . F 6 HOH A 10 410 611 HOH HOH . F 6 HOH A 11 411 612 HOH HOH . F 6 HOH A 12 412 613 HOH HOH . F 6 HOH A 13 413 614 HOH HOH . F 6 HOH A 14 414 617 HOH HOH . F 6 HOH A 15 415 618 HOH HOH . F 6 HOH A 16 416 619 HOH HOH . F 6 HOH A 17 417 621 HOH HOH . F 6 HOH A 18 418 622 HOH HOH . F 6 HOH A 19 419 623 HOH HOH . F 6 HOH A 20 420 624 HOH HOH . F 6 HOH A 21 421 625 HOH HOH . F 6 HOH A 22 422 626 HOH HOH . F 6 HOH A 23 423 629 HOH HOH . F 6 HOH A 24 424 630 HOH HOH . F 6 HOH A 25 425 633 HOH HOH . F 6 HOH A 26 426 636 HOH HOH . F 6 HOH A 27 427 701 HOH HOH . F 6 HOH A 28 428 703 HOH HOH . F 6 HOH A 29 429 704 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 5 52.193 24.227 13.97 1 69.62 ? C1 L2P 303 A 1 HETATM 2 O O1 L2P . . . E 5 52.732 25.145 12.986 1 70.87 ? O1 L2P 303 A 1 HETATM 3 C C2 L2P . . . E 5 50.617 24.122 13.912 1 68.95 ? C2 L2P 303 A 1 HETATM 4 O O2 L2P . . . E 5 50.175 23.144 14.976 1 67.39 ? O2 L2P 303 A 1 HETATM 5 C C3 L2P . . . E 5 50.221 23.582 12.483 1 69.81 ? C3 L2P 303 A 1 HETATM 6 O O3 L2P . . . E 5 49.907 24.529 11.58 1 70.86 ? O3 L2P 303 A 1 HETATM 7 C C11 L2P . . . E 5 53.361 26.17 13.645 1 71.92 ? C11 L2P 303 A 1 HETATM 8 C C12 L2P . . . E 5 54.869 26.085 13.618 1 72.79 ? C12 L2P 303 A 1 HETATM 9 C C13 L2P . . . E 5 55.535 27.24 14.37 1 73.33 ? C13 L2P 303 A 1 HETATM 10 C C14 L2P . . . E 5 56.528 27.781 13.402 1 73.55 ? C14 L2P 303 A 1 HETATM 11 C C15 L2P . . . E 5 56.313 26.786 15.68 1 74.32 ? C15 L2P 303 A 1 HETATM 12 C C16 L2P . . . E 5 55.345 26.718 16.888 1 75.6 ? C16 L2P 303 A 1 HETATM 13 C C17 L2P . . . E 5 55.847 25.927 18.126 1 76.93 ? C17 L2P 303 A 1 HETATM 14 C C18 L2P . . . E 5 55.135 26.584 19.307 1 77.88 ? C18 L2P 303 A 1 HETATM 15 C C19 L2P . . . E 5 56.127 27.382 20.182 1 77.93 ? C19 L2P 303 A 1 HETATM 16 C C20 L2P . . . E 5 54.445 25.579 20.316 1 78.91 ? C20 L2P 303 A 1 HETATM 17 C C21 L2P . . . E 5 52.92 25.254 20.461 1 80.23 ? C21 L2P 303 A 1 HETATM 18 C C22 L2P . . . E 5 52.679 26.27 21.614 1 81.38 ? C22 L2P 303 A 1 HETATM 19 C C23 L2P . . . E 5 51.287 26.629 22.455 1 82.31 ? C23 L2P 303 A 1 HETATM 20 C C24 L2P . . . E 5 51.933 27.756 23.405 1 82.41 ? C24 L2P 303 A 1 HETATM 21 C C25 L2P . . . E 5 50.741 25.4 23.418 1 82.78 ? C25 L2P 303 A 1 HETATM 22 C C26 L2P . . . E 5 49.73 26.079 24.608 1 83.7 ? C26 L2P 303 A 1 HETATM 23 C C27 L2P . . . E 5 50.089 25.836 26.137 1 84.1 ? C27 L2P 303 A 1 HETATM 24 C C28 L2P . . . E 5 49.043 26.553 27.172 1 84.19 ? C28 L2P 303 A 1 HETATM 25 C C29 L2P . . . E 5 48.817 25.749 28.518 1 84.19 ? C29 L2P 303 A 1 HETATM 26 C C30 L2P . . . E 5 49.551 28.027 27.574 1 84.32 ? C30 L2P 303 A 1 HETATM 27 C C41 L2P . . . E 5 50.457 23.476 16.417 1 65.11 ? C41 L2P 303 A 1 HETATM 28 C C42 L2P . . . E 5 50.027 22.159 17.226 1 62.96 ? C42 L2P 303 A 1 HETATM 29 C C43 L2P . . . E 5 50.131 22.189 18.848 1 61.7 ? C43 L2P 303 A 1 HETATM 30 C C44 L2P . . . E 5 49.627 23.527 19.51 1 61.47 ? C44 L2P 303 A 1 HETATM 31 C C45 L2P . . . E 5 51.656 21.871 19.179 1 60.41 ? C45 L2P 303 A 1 HETATM 32 C C46 L2P . . . E 5 51.952 20.606 20.058 1 59.64 ? C46 L2P 303 A 1 HETATM 33 C C47 L2P . . . E 5 51.591 20.993 21.521 1 58.68 ? C47 L2P 303 A 1 HETATM 34 C C48 L2P . . . E 5 51.794 19.848 22.751 1 57.99 ? C48 L2P 303 A 1 HETATM 35 C C49 L2P . . . E 5 50.787 18.645 22.622 1 57.5 ? C49 L2P 303 A 1 HETATM 36 C C50 L2P . . . E 5 51.646 20.741 24.124 1 57.32 ? C50 L2P 303 A 1 HETATM 37 C C51 L2P . . . E 5 51.749 20.163 25.594 1 56.53 ? C51 L2P 303 A 1 HETATM 38 C C52 L2P . . . E 5 51.574 21.352 26.58 1 56.46 ? C52 L2P 303 A 1 HETATM 39 C C53 L2P . . . E 5 51.145 21.12 28.06 1 56.45 ? C53 L2P 303 A 1 HETATM 40 C C54 L2P . . . E 5 50.132 22.222 28.223 1 56.82 ? C54 L2P 303 A 1 HETATM 41 C C55 L2P . . . E 5 52.391 21.317 29.059 1 56.6 ? C55 L2P 303 A 1 HETATM 42 C C56 L2P . . . E 5 52.217 22.319 30.295 1 57.47 ? C56 L2P 303 A 1 HETATM 43 C C57 L2P . . . E 5 53.549 22.419 31.194 1 57.44 ? C57 L2P 303 A 1 HETATM 44 C C58 L2P . . . E 5 53.386 23.411 32.401 1 58.11 ? C58 L2P 303 A 1 HETATM 45 C C59 L2P . . . E 5 53.285 22.599 33.608 1 57.77 ? C59 L2P 303 A 1 HETATM 46 C C60 L2P . . . E 5 54.615 24.375 32.491 1 57.99 ? C60 L2P 303 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 46 #