data_2ZFE # _model_server_result.job_id hFsUMl3id7CnMe45c-dnpA _model_server_result.datetime_utc '2024-11-27 22:07:41' _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 2zfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":280}' # _entry.id 2ZFE # _exptl.entry_id 2ZFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 733.137 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-PHOSPHORYL-[1,2-DI-PHYTANYL]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 90 _cell.angle_gamma 120 _cell.entry_id 2ZFE _cell.length_a 102.41 _cell.length_b 102.41 _cell.length_c 112.47 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZFE _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,G,H,I,J _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 1 102.41 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 51.205 88.689662 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N ? 6 H N 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 SGA . B SGA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? # _chem_comp.formula 'C43 H89 O6 P' _chem_comp.formula_weight 733.137 _chem_comp.id L1P _chem_comp.mon_nstd_flag . _chem_comp.name 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE # 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 L1P sing 163 n n C1 C2 L1P sing 164 n n C1 H12 L1P sing 165 n n C1 H11 L1P sing 166 n n O1 C11 L1P sing 167 n n C2 O2 L1P sing 168 n n C2 C3 L1P sing 169 n n C2 H2 L1P sing 170 n n O2 C41 L1P sing 171 n n C3 O3 L1P sing 172 n n C3 H32 L1P sing 173 n n C3 H31 L1P sing 174 n n O3 P L1P sing 175 n n P O1P L1P doub 176 n n P O2P L1P sing 177 n n P O3P L1P sing 178 n n O2P HOP2 L1P sing 179 n n O3P HOP3 L1P sing 180 n n C11 C12 L1P sing 181 n n C11 H112 L1P sing 182 n n C11 H111 L1P sing 183 n n C12 C13 L1P sing 184 n n C12 H122 L1P sing 185 n n C12 H121 L1P sing 186 n n C13 C14 L1P sing 187 n n C13 C15 L1P sing 188 n n C13 H13 L1P sing 189 n n C14 H143 L1P sing 190 n n C14 H142 L1P sing 191 n n C14 H141 L1P sing 192 n n C15 C16 L1P sing 193 n n C15 H152 L1P sing 194 n n C15 H151 L1P sing 195 n n C16 C17 L1P sing 196 n n C16 H162 L1P sing 197 n n C16 H161 L1P sing 198 n n C17 C18 L1P sing 199 n n C17 H172 L1P sing 200 n n C17 H171 L1P sing 201 n n C18 C19 L1P sing 202 n n C18 C20 L1P sing 203 n n C18 H18 L1P sing 204 n n C19 H193 L1P sing 205 n n C19 H192 L1P sing 206 n n C19 H191 L1P sing 207 n n C20 C21 L1P sing 208 n n C20 H202 L1P sing 209 n n C20 H201 L1P sing 210 n n C21 C22 L1P sing 211 n n C21 H212 L1P sing 212 n n C21 H211 L1P sing 213 n n C22 C23 L1P sing 214 n n C22 H222 L1P sing 215 n n C22 H221 L1P sing 216 n n C23 C24 L1P sing 217 n n C23 C25 L1P sing 218 n n C23 H23 L1P sing 219 n n C24 H243 L1P sing 220 n n C24 H242 L1P sing 221 n n C24 H241 L1P sing 222 n n C25 C26 L1P sing 223 n n C25 H252 L1P sing 224 n n C25 H251 L1P sing 225 n n C26 C27 L1P sing 226 n n C26 H262 L1P sing 227 n n C26 H261 L1P sing 228 n n C27 C28 L1P sing 229 n n C27 H272 L1P sing 230 n n C27 H271 L1P sing 231 n n C28 C29 L1P sing 232 n n C28 C30 L1P sing 233 n n C28 H28 L1P sing 234 n n C29 H293 L1P sing 235 n n C29 H292 L1P sing 236 n n C29 H291 L1P sing 237 n n C30 H303 L1P sing 238 n n C30 H302 L1P sing 239 n n C30 H301 L1P sing 240 n n C41 C42 L1P sing 241 n n C41 H412 L1P sing 242 n n C41 H411 L1P sing 243 n n C42 C43 L1P sing 244 n n C42 H422 L1P sing 245 n n C42 H421 L1P sing 246 n n C43 C44 L1P sing 247 n n C43 C45 L1P sing 248 n n C43 H43 L1P sing 249 n n C44 H443 L1P sing 250 n n C44 H442 L1P sing 251 n n C44 H441 L1P sing 252 n n C45 C46 L1P sing 253 n n C45 H452 L1P sing 254 n n C45 H451 L1P sing 255 n n C46 C47 L1P sing 256 n n C46 H462 L1P sing 257 n n C46 H461 L1P sing 258 n n C47 C48 L1P sing 259 n n C47 H472 L1P sing 260 n n C47 H471 L1P sing 261 n n C48 C49 L1P sing 262 n n C48 C50 L1P sing 263 n n C48 H48 L1P sing 264 n n C49 H493 L1P sing 265 n n C49 H492 L1P sing 266 n n C49 H491 L1P sing 267 n n C50 C51 L1P sing 268 n n C50 H502 L1P sing 269 n n C50 H501 L1P sing 270 n n C51 C52 L1P sing 271 n n C51 H512 L1P sing 272 n n C51 H511 L1P sing 273 n n C52 C53 L1P sing 274 n n C52 H522 L1P sing 275 n n C52 H521 L1P sing 276 n n C53 C54 L1P sing 277 n n C53 C55 L1P sing 278 n n C53 H53 L1P sing 279 n n C54 H543 L1P sing 280 n n C54 H542 L1P sing 281 n n C54 H541 L1P sing 282 n n C55 C56 L1P sing 283 n n C55 H552 L1P sing 284 n n C55 H551 L1P sing 285 n n C56 C57 L1P sing 286 n n C56 H562 L1P sing 287 n n C56 H561 L1P sing 288 n n C57 C58 L1P sing 289 n n C57 H572 L1P sing 290 n n C57 H571 L1P sing 291 n n C58 C59 L1P sing 292 n n C58 C60 L1P sing 293 n n C58 H58 L1P sing 294 n n C59 H593 L1P sing 295 n n C59 H592 L1P sing 296 n n C59 H591 L1P sing 297 n n C60 H603 L1P sing 298 n n C60 H602 L1P sing 299 n n C60 H601 L1P sing 300 n n # _atom_sites.entry_id 2ZFE _atom_sites.fract_transf_matrix[1][1] 0.009765 _atom_sites.fract_transf_matrix[1][2] 0.005638 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011275 _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] 0.008891 _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 L3P A 1 260 260 L3P L1P . E 5 L2P A 1 270 270 L2P LP2 . F 6 L1P A 1 280 280 L1P L1P . G 6 L1P A 1 290 290 L1P L1P . H 6 L1P A 1 300 300 L1P L1P . I 7 XE A 1 638 638 XE XE . J 8 HOH A 1 600 600 HOH HOH . J 8 HOH A 2 601 601 HOH HOH . J 8 HOH A 3 602 602 HOH HOH . J 8 HOH A 4 603 603 HOH HOH . J 8 HOH A 5 604 604 HOH HOH . J 8 HOH A 6 605 605 HOH HOH . J 8 HOH A 7 606 606 HOH HOH . J 8 HOH A 8 607 607 HOH HOH . J 8 HOH A 9 608 608 HOH HOH . J 8 HOH A 10 609 609 HOH HOH . J 8 HOH A 11 610 610 HOH HOH . J 8 HOH A 12 611 611 HOH HOH . J 8 HOH A 13 612 612 HOH HOH . J 8 HOH A 14 613 613 HOH HOH . J 8 HOH A 15 614 614 HOH HOH . J 8 HOH A 16 615 615 HOH HOH . J 8 HOH A 17 616 616 HOH HOH . J 8 HOH A 18 617 617 HOH HOH . J 8 HOH A 19 618 618 HOH HOH . J 8 HOH A 20 619 619 HOH HOH . J 8 HOH A 21 620 620 HOH HOH . J 8 HOH A 22 621 621 HOH HOH . J 8 HOH A 23 622 622 HOH HOH . J 8 HOH A 24 623 623 HOH HOH . J 8 HOH A 25 624 624 HOH HOH . J 8 HOH A 26 625 625 HOH HOH . J 8 HOH A 27 626 626 HOH HOH . J 8 HOH A 28 627 627 HOH HOH . J 8 HOH A 29 628 628 HOH HOH . J 8 HOH A 30 629 629 HOH HOH . J 8 HOH A 31 630 630 HOH HOH . J 8 HOH A 32 631 631 HOH HOH . J 8 HOH A 33 632 632 HOH HOH . J 8 HOH A 34 633 633 HOH HOH . J 8 HOH A 35 634 634 HOH HOH . J 8 HOH A 36 635 635 HOH HOH . J 8 HOH A 37 636 636 HOH HOH . J 8 HOH A 38 637 637 HOH HOH . J 8 HOH A 39 639 639 HOH HOH . J 8 HOH A 40 640 640 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 L1P . . . F 6 25.9 38.148 10.585 1 128.4 ? C1 L1P 280 A 1 HETATM 2 O O1 L1P . . . F 6 25.103 38.736 11.693 1 128.6 ? O1 L1P 280 A 1 HETATM 3 C C2 L1P . . . F 6 27.46 37.997 10.949 1 127.79 ? C2 L1P 280 A 1 HETATM 4 O O2 L1P . . . F 6 28 39.427 11.317 1 126.45 ? O2 L1P 280 A 1 HETATM 5 C C3 L1P . . . F 6 28.337 37.357 9.748 1 128.11 ? C3 L1P 280 A 1 HETATM 6 O O3 L1P . . . F 6 27.929 35.999 9.312 1 128.5 ? O3 L1P 280 A 1 HETATM 7 P P L1P . . . F 6 27.506 35.763 7.707 1 128.95 ? P L1P 280 A 1 HETATM 8 O O1P L1P . . . F 6 26.304 36.611 7.387 1 129.02 ? O1P L1P 280 A 1 HETATM 9 O O2P L1P . . . F 6 27.131 34.33 7.468 1 128.6 ? O2P L1P 280 A 1 HETATM 10 O O3P L1P . . . F 6 28.819 36.223 6.729 1 128.64 ? O3P L1P 280 A 1 HETATM 11 C C11 L1P . . . F 6 23.701 38.895 11.419 1 128.37 ? C11 L1P 280 A 1 HETATM 12 C C12 L1P . . . F 6 22.842 38.049 12.429 1 128.3 ? C12 L1P 280 A 1 HETATM 13 C C13 L1P . . . F 6 22.311 38.683 13.819 1 128.18 ? C13 L1P 280 A 1 HETATM 14 C C14 L1P . . . F 6 21.513 40.02 13.671 1 128.41 ? C14 L1P 280 A 1 HETATM 15 C C15 L1P . . . F 6 23.542 38.908 14.788 1 127.71 ? C15 L1P 280 A 1 HETATM 16 C C16 L1P . . . F 6 23.536 37.988 16.063 1 127.15 ? C16 L1P 280 A 1 HETATM 17 C C17 L1P . . . F 6 24.804 38.32 16.922 1 126.79 ? C17 L1P 280 A 1 HETATM 18 C C18 L1P . . . F 6 25.082 37.392 18.128 1 126.35 ? C18 L1P 280 A 1 HETATM 19 C C19 L1P . . . F 6 25.369 38.217 19.399 1 126.21 ? C19 L1P 280 A 1 HETATM 20 C C20 L1P . . . F 6 26.291 36.529 17.897 1 126.17 ? C20 L1P 280 A 1 HETATM 21 C C41 L1P . . . F 6 28.7 39.527 12.644 1 124.43 ? C41 L1P 280 A 1 HETATM 22 C C42 L1P . . . F 6 27.904 40.362 13.728 1 122.2 ? C42 L1P 280 A 1 HETATM 23 C C43 L1P . . . F 6 28.627 41.279 14.808 1 120.58 ? C43 L1P 280 A 1 HETATM 24 C C44 L1P . . . F 6 29.67 42.26 14.207 1 120.5 ? C44 L1P 280 A 1 HETATM 25 C C45 L1P . . . F 6 29.363 40.421 15.87 1 119.16 ? C45 L1P 280 A 1 HETATM 26 C C46 L1P . . . F 6 28.539 40.135 17.165 1 117.61 ? C46 L1P 280 A 1 HETATM 27 C C47 L1P . . . F 6 28.823 41.247 18.245 1 115.92 ? C47 L1P 280 A 1 HETATM 28 C C48 L1P . . . F 6 29.58 40.845 19.538 1 114.42 ? C48 L1P 280 A 1 HETATM 29 C C49 L1P . . . F 6 28.548 40.275 20.523 1 114.44 ? C49 L1P 280 A 1 HETATM 30 C C50 L1P . . . F 6 30.335 42.185 19.976 1 113.55 ? C50 L1P 280 A 1 HETATM 31 C C51 L1P . . . F 6 30.165 42.929 21.194 1 112.51 ? C51 L1P 280 A 1 HETATM 32 C C52 L1P . . . F 6 31.073 44.214 21.312 1 111.76 ? C52 L1P 280 A 1 HETATM 33 C C53 L1P . . . F 6 31.577 44.793 22.76 1 111.12 ? C53 L1P 280 A 1 HETATM 34 C C54 L1P . . . F 6 32.434 43.807 23.566 1 110.78 ? C54 L1P 280 A 1 HETATM 35 C C55 L1P . . . F 6 30.309 45.233 23.651 1 110.94 ? C55 L1P 280 A 1 HETATM 36 C C56 L1P . . . F 6 30.513 45.852 25.143 1 110.15 ? C56 L1P 280 A 1 HETATM 37 C C57 L1P . . . F 6 29.094 46.206 25.811 1 109.21 ? C57 L1P 280 A 1 HETATM 38 C C58 L1P . . . F 6 28.863 45.493 27.168 1 108.65 ? C58 L1P 280 A 1 HETATM 39 C C59 L1P . . . F 6 28.549 46.534 28.223 1 108.73 ? C59 L1P 280 A 1 HETATM 40 C C60 L1P . . . F 6 27.696 44.521 27.067 1 108.24 ? C60 L1P 280 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #