data_3VHZ # _model_server_result.job_id 7xvI4xyQPb5bzwPwcAr3XQ _model_server_result.datetime_utc '2024-10-18 20:26:51' _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 3vhz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":270}' # _entry.id 3VHZ # _exptl.entry_id 3VHZ _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 3VHZ _cell.length_a 102.6 _cell.length_b 102.6 _cell.length_c 112.34 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VHZ _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 1 102.6 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 51.3 88.854206 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 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 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 3VHZ _atom_sites.fract_transf_matrix[1][1] 0.009747 _atom_sites.fract_transf_matrix[1][2] 0.005627 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011254 _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] 0.008902 _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 1 250 250 RET RET . D 4 SOG A 1 430 430 SOG SOG . E 5 L2P A 1 270 270 L2P L2P . F 6 HOH A 1 600 600 HOH HOH . F 6 HOH A 2 601 601 HOH HOH . F 6 HOH A 3 602 602 HOH HOH . F 6 HOH A 4 603 603 HOH HOH . F 6 HOH A 5 604 604 HOH HOH . F 6 HOH A 6 605 605 HOH HOH . F 6 HOH A 7 606 606 HOH HOH . F 6 HOH A 8 607 607 HOH HOH . F 6 HOH A 9 608 608 HOH HOH . F 6 HOH A 10 609 609 HOH HOH . F 6 HOH A 11 610 610 HOH HOH . F 6 HOH A 12 611 611 HOH HOH . F 6 HOH A 13 612 612 HOH HOH . F 6 HOH A 14 613 613 HOH HOH . F 6 HOH A 15 614 614 HOH HOH . F 6 HOH A 16 615 615 HOH HOH . F 6 HOH A 17 616 616 HOH HOH . F 6 HOH A 18 617 617 HOH HOH . F 6 HOH A 19 618 618 HOH HOH . F 6 HOH A 20 619 619 HOH HOH . F 6 HOH A 21 621 621 HOH HOH . F 6 HOH A 22 622 622 HOH HOH . F 6 HOH A 23 623 623 HOH HOH . F 6 HOH A 24 624 624 HOH HOH . F 6 HOH A 25 625 625 HOH HOH . F 6 HOH A 26 626 626 HOH HOH . F 6 HOH A 27 627 627 HOH HOH . F 6 HOH A 28 628 628 HOH HOH . F 6 HOH A 29 629 629 HOH HOH . F 6 HOH A 30 630 630 HOH HOH . F 6 HOH A 31 631 631 HOH HOH . F 6 HOH A 32 632 632 HOH HOH . F 6 HOH A 33 633 633 HOH HOH . F 6 HOH A 34 635 635 HOH HOH . F 6 HOH A 35 636 636 HOH HOH . F 6 HOH A 36 637 637 HOH HOH . F 6 HOH A 37 638 638 HOH HOH . F 6 HOH A 38 639 639 HOH HOH . F 6 HOH A 39 640 640 HOH HOH . F 6 HOH A 40 701 701 HOH HOH . F 6 HOH A 41 702 702 HOH HOH . F 6 HOH A 42 703 703 HOH HOH . F 6 HOH A 43 704 704 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 52.352 24.249 13.944 1 78.63 ? C1 L2P 270 A 1 HETATM 2 O O1 L2P . . . E 5 53.045 24.983 12.899 1 80.14 ? O1 L2P 270 A 1 HETATM 3 C C2 L2P . . . E 5 50.774 24.257 13.779 1 77.5 ? C2 L2P 270 A 1 HETATM 4 O O2 L2P . . . E 5 50.182 23.462 14.925 1 75.11 ? O2 L2P 270 A 1 HETATM 5 C C3 L2P . . . E 5 50.425 23.571 12.395 1 79.29 ? C3 L2P 270 A 1 HETATM 6 O O3 L2P . . . E 5 50.089 24.43 11.41 1 80.71 ? O3 L2P 270 A 1 HETATM 7 C C11 L2P . . . E 5 53.516 26.159 13.431 1 82.64 ? C11 L2P 270 A 1 HETATM 8 C C12 L2P . . . E 5 55.016 26.206 13.59 1 84.34 ? C12 L2P 270 A 1 HETATM 9 C C13 L2P . . . E 5 55.502 27.53 14.196 1 85.42 ? C13 L2P 270 A 1 HETATM 10 C C14 L2P . . . E 5 56.442 28.081 13.179 1 85.39 ? C14 L2P 270 A 1 HETATM 11 C C15 L2P . . . E 5 56.302 27.356 15.557 1 87.35 ? C15 L2P 270 A 1 HETATM 12 C C16 L2P . . . E 5 55.366 27.579 16.772 1 89.47 ? C16 L2P 270 A 1 HETATM 13 C C17 L2P . . . E 5 55.173 26.353 17.709 1 91.96 ? C17 L2P 270 A 1 HETATM 14 C C18 L2P . . . E 5 56.144 26.609 18.866 1 93.77 ? C18 L2P 270 A 1 HETATM 15 C C19 L2P . . . E 5 57.297 25.577 18.881 1 93.92 ? C19 L2P 270 A 1 HETATM 16 C C20 L2P . . . E 5 55.51 26.514 20.315 1 95 ? C20 L2P 270 A 1 HETATM 17 C C21 L2P . . . E 5 54.358 25.571 20.793 1 96.52 ? C21 L2P 270 A 1 HETATM 18 C C22 L2P . . . E 5 53.406 26.738 21.169 1 97.69 ? C22 L2P 270 A 1 HETATM 19 C C23 L2P . . . E 5 51.874 26.671 21.791 1 98.8 ? C23 L2P 270 A 1 HETATM 20 C C24 L2P . . . E 5 51.596 28.244 21.892 1 99.45 ? C24 L2P 270 A 1 HETATM 21 C C25 L2P . . . E 5 51.799 26.069 23.303 1 99.35 ? C25 L2P 270 A 1 HETATM 22 C C26 L2P . . . E 5 50.931 24.633 23.176 1 99.98 ? C26 L2P 270 A 1 HETATM 23 C C27 L2P . . . E 5 49.362 24.752 23.106 1 100.87 ? C27 L2P 270 A 1 HETATM 24 C C28 L2P . . . E 5 48.627 23.309 22.974 1 101.27 ? C28 L2P 270 A 1 HETATM 25 C C29 L2P . . . E 5 48.606 22.483 24.318 1 101.7 ? C29 L2P 270 A 1 HETATM 26 C C30 L2P . . . E 5 47.104 23.483 22.488 1 101.6 ? C30 L2P 270 A 1 HETATM 27 C C41 L2P . . . E 5 50.392 23.965 16.331 1 72.12 ? C41 L2P 270 A 1 HETATM 28 C C42 L2P . . . E 5 50.956 22.71 17.168 1 69.76 ? C42 L2P 270 A 1 HETATM 29 C C43 L2P . . . E 5 50.486 22.57 18.721 1 68.44 ? C43 L2P 270 A 1 HETATM 30 C C44 L2P . . . E 5 50.342 23.941 19.482 1 67.53 ? C44 L2P 270 A 1 HETATM 31 C C45 L2P . . . E 5 51.543 21.596 19.408 1 67.35 ? C45 L2P 270 A 1 HETATM 32 C C46 L2P . . . E 5 51.042 20.805 20.67 1 67 ? C46 L2P 270 A 1 HETATM 33 C C47 L2P . . . E 5 52.311 20.312 21.425 1 65.92 ? C47 L2P 270 A 1 HETATM 34 C C48 L2P . . . E 5 52.11 19.415 22.851 1 65.84 ? C48 L2P 270 A 1 HETATM 35 C C49 L2P . . . E 5 50.923 18.389 22.769 1 65.25 ? C49 L2P 270 A 1 HETATM 36 C C50 L2P . . . E 5 51.964 20.545 24.04 1 64.75 ? C50 L2P 270 A 1 HETATM 37 C C51 L2P . . . E 5 51.755 20.184 25.571 1 64.18 ? C51 L2P 270 A 1 HETATM 38 C C52 L2P . . . E 5 51.681 21.504 26.384 1 64.82 ? C52 L2P 270 A 1 HETATM 39 C C53 L2P . . . E 5 51.04 21.534 27.805 1 64.83 ? C53 L2P 270 A 1 HETATM 40 C C54 L2P . . . E 5 50.197 22.779 27.721 1 65.24 ? C54 L2P 270 A 1 HETATM 41 C C55 L2P . . . E 5 52.144 21.707 28.945 1 64.72 ? C55 L2P 270 A 1 HETATM 42 C C56 L2P . . . E 5 51.599 21.919 30.427 1 65.92 ? C56 L2P 270 A 1 HETATM 43 C C57 L2P . . . E 5 52.79 22.093 31.491 1 66.58 ? C57 L2P 270 A 1 HETATM 44 C C58 L2P . . . E 5 52.269 22.295 32.96 1 67.56 ? C58 L2P 270 A 1 HETATM 45 C C59 L2P . . . E 5 53.099 21.452 33.813 1 68.36 ? C59 L2P 270 A 1 HETATM 46 C C60 L2P . . . E 5 52.397 23.782 33.39 1 67.51 ? C60 L2P 270 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #