data_1DZE # _model_server_result.job_id O_RbOc3eSgOAJrhS0_2_OQ _model_server_result.datetime_utc '2024-11-18 00:44:04' _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 1dze # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":260}' # _entry.id 1DZE # _exptl.entry_id 1DZE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 733.137 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-PHOSPHORYL-[1,2-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 1DZE _cell.length_a 102.4 _cell.length_b 102.4 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DZE _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 PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.2 88.681001 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.4 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 GAL 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 A 400 GLC 2 n B MAN 2 B 2 MAN A 410 MAN 2 n B GAL 3 B 3 GAL A 420 GAL # 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 216 A LYS 216 1_555 C C15 RET . A RET 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 187 n n C1 C2 L1P sing 188 n n C1 H12 L1P sing 189 n n C1 H11 L1P sing 190 n n O1 C11 L1P sing 191 n n C2 O2 L1P sing 192 n n C2 C3 L1P sing 193 n n C2 H2 L1P sing 194 n n O2 C41 L1P sing 195 n n C3 O3 L1P sing 196 n n C3 H32 L1P sing 197 n n C3 H31 L1P sing 198 n n O3 P L1P sing 199 n n P O1P L1P doub 200 n n P O2P L1P sing 201 n n P O3P L1P sing 202 n n O2P HOP2 L1P sing 203 n n O3P HOP3 L1P sing 204 n n C11 C12 L1P sing 205 n n C11 H112 L1P sing 206 n n C11 H111 L1P sing 207 n n C12 C13 L1P sing 208 n n C12 H122 L1P sing 209 n n C12 H121 L1P sing 210 n n C13 C14 L1P sing 211 n n C13 C15 L1P sing 212 n n C13 H13 L1P sing 213 n n C14 H143 L1P sing 214 n n C14 H142 L1P sing 215 n n C14 H141 L1P sing 216 n n C15 C16 L1P sing 217 n n C15 H152 L1P sing 218 n n C15 H151 L1P sing 219 n n C16 C17 L1P sing 220 n n C16 H162 L1P sing 221 n n C16 H161 L1P sing 222 n n C17 C18 L1P sing 223 n n C17 H172 L1P sing 224 n n C17 H171 L1P sing 225 n n C18 C19 L1P sing 226 n n C18 C20 L1P sing 227 n n C18 H18 L1P sing 228 n n C19 H193 L1P sing 229 n n C19 H192 L1P sing 230 n n C19 H191 L1P sing 231 n n C20 C21 L1P sing 232 n n C20 H202 L1P sing 233 n n C20 H201 L1P sing 234 n n C21 C22 L1P sing 235 n n C21 H212 L1P sing 236 n n C21 H211 L1P sing 237 n n C22 C23 L1P sing 238 n n C22 H222 L1P sing 239 n n C22 H221 L1P sing 240 n n C23 C24 L1P sing 241 n n C23 C25 L1P sing 242 n n C23 H23 L1P sing 243 n n C24 H243 L1P sing 244 n n C24 H242 L1P sing 245 n n C24 H241 L1P sing 246 n n C25 C26 L1P sing 247 n n C25 H252 L1P sing 248 n n C25 H251 L1P sing 249 n n C26 C27 L1P sing 250 n n C26 H262 L1P sing 251 n n C26 H261 L1P sing 252 n n C27 C28 L1P sing 253 n n C27 H272 L1P sing 254 n n C27 H271 L1P sing 255 n n C28 C29 L1P sing 256 n n C28 C30 L1P sing 257 n n C28 H28 L1P sing 258 n n C29 H293 L1P sing 259 n n C29 H292 L1P sing 260 n n C29 H291 L1P sing 261 n n C30 H303 L1P sing 262 n n C30 H302 L1P sing 263 n n C30 H301 L1P sing 264 n n C41 C42 L1P sing 265 n n C41 H412 L1P sing 266 n n C41 H411 L1P sing 267 n n C42 C43 L1P sing 268 n n C42 H422 L1P sing 269 n n C42 H421 L1P sing 270 n n C43 C44 L1P sing 271 n n C43 C45 L1P sing 272 n n C43 H43 L1P sing 273 n n C44 H443 L1P sing 274 n n C44 H442 L1P sing 275 n n C44 H441 L1P sing 276 n n C45 C46 L1P sing 277 n n C45 H452 L1P sing 278 n n C45 H451 L1P sing 279 n n C46 C47 L1P sing 280 n n C46 H462 L1P sing 281 n n C46 H461 L1P sing 282 n n C47 C48 L1P sing 283 n n C47 H472 L1P sing 284 n n C47 H471 L1P sing 285 n n C48 C49 L1P sing 286 n n C48 C50 L1P sing 287 n n C48 H48 L1P sing 288 n n C49 H493 L1P sing 289 n n C49 H492 L1P sing 290 n n C49 H491 L1P sing 291 n n C50 C51 L1P sing 292 n n C50 H502 L1P sing 293 n n C50 H501 L1P sing 294 n n C51 C52 L1P sing 295 n n C51 H512 L1P sing 296 n n C51 H511 L1P sing 297 n n C52 C53 L1P sing 298 n n C52 H522 L1P sing 299 n n C52 H521 L1P sing 300 n n C53 C54 L1P sing 301 n n C53 C55 L1P sing 302 n n C53 H53 L1P sing 303 n n C54 H543 L1P sing 304 n n C54 H542 L1P sing 305 n n C54 H541 L1P sing 306 n n C55 C56 L1P sing 307 n n C55 H552 L1P sing 308 n n C55 H551 L1P sing 309 n n C56 C57 L1P sing 310 n n C56 H562 L1P sing 311 n n C56 H561 L1P sing 312 n n C57 C58 L1P sing 313 n n C57 H572 L1P sing 314 n n C57 H571 L1P sing 315 n n C58 C59 L1P sing 316 n n C58 C60 L1P sing 317 n n C58 H58 L1P sing 318 n n C59 H593 L1P sing 319 n n C59 H592 L1P sing 320 n n C59 H591 L1P sing 321 n n C60 H603 L1P sing 322 n n C60 H602 L1P sing 323 n n C60 H601 L1P sing 324 n n # _atom_sites.entry_id 1DZE _atom_sites.fract_transf_matrix[1][1] 0.009766 _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] 0.011276 _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 1 250 250 RET RET . D 4 L1P A 1 260 260 L1P L1P . E 5 L2P A 1 270 270 L2P L2P . F 6 L3P A 1 280 280 L3P L3P . G 7 L4P A 1 290 290 L4P L4P . H 5 L2P A 1 300 300 L2P L2P . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . I 8 HOH A 9 2009 2009 HOH HOH . I 8 HOH A 10 2010 2010 HOH HOH . I 8 HOH A 11 2011 2011 HOH HOH . I 8 HOH A 12 2012 2012 HOH HOH . I 8 HOH A 13 2013 2013 HOH HOH . I 8 HOH A 14 2014 2014 HOH HOH . I 8 HOH A 15 2015 2015 HOH HOH . I 8 HOH A 16 2016 2016 HOH HOH . I 8 HOH A 17 2017 2017 HOH HOH . I 8 HOH A 18 2018 2018 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 . . . D 4 36.991 39.705 40.663 1 75.5 ? C1 L1P 260 A 1 HETATM 2 O O1 L1P . . . D 4 35.667 39.23 40.427 1 61.7 ? O1 L1P 260 A 1 HETATM 3 C C2 L1P . . . D 4 36.941 41.103 41.287 1 89.22 ? C2 L1P 260 A 1 HETATM 4 O O2 L1P . . . D 4 36.421 42.035 40.319 1 96.68 ? O2 L1P 260 A 1 HETATM 5 C C3 L1P . . . D 4 38.364 41.506 41.708 1 94.48 ? C3 L1P 260 A 1 HETATM 6 O O3 L1P . . . D 4 38.319 42.568 42.68 1 100 ? O3 L1P 260 A 1 HETATM 7 P P L1P . . . D 4 38.06 42.266 44.251 1 100 ? P L1P 260 A 1 HETATM 8 O O1P L1P . . . D 4 37.781 43.539 44.956 1 100 ? O1P L1P 260 A 1 HETATM 9 O O2P L1P . . . D 4 39.259 41.631 44.85 1 100 ? O2P L1P 260 A 1 HETATM 10 O O3P L1P . . . D 4 36.79 41.289 44.408 1 100 ? O3P L1P 260 A 1 HETATM 11 C C11 L1P . . . D 4 35.442 38.246 39.42 1 51.04 ? C11 L1P 260 A 1 HETATM 12 C C12 L1P . . . D 4 35.206 38.941 38.074 1 60.21 ? C12 L1P 260 A 1 HETATM 13 C C13 L1P . . . D 4 35.564 37.978 36.942 1 60.99 ? C13 L1P 260 A 1 HETATM 14 C C14 L1P . . . D 4 36.681 37.056 37.404 1 73.43 ? C14 L1P 260 A 1 HETATM 15 C C15 L1P . . . D 4 36.069 38.769 35.738 1 61.93 ? C15 L1P 260 A 1 HETATM 16 C C16 L1P . . . D 4 36.694 37.798 34.735 1 65.61 ? C16 L1P 260 A 1 HETATM 17 C C17 L1P . . . D 4 37.446 38.59 33.672 1 71.44 ? C17 L1P 260 A 1 HETATM 18 C C18 L1P . . . D 4 36.486 38.912 32.53 1 75.16 ? C18 L1P 260 A 1 HETATM 19 C C19 L1P . . . D 4 35.982 37.609 31.913 1 81.47 ? C19 L1P 260 A 1 HETATM 20 C C20 L1P . . . D 4 37.22 39.722 31.466 1 80.08 ? C20 L1P 260 A 1 HETATM 21 C C21 L1P . . . D 4 36.305 40.846 30.983 1 84.74 ? C21 L1P 260 A 1 HETATM 22 C C22 L1P . . . D 4 36.682 41.231 29.553 1 89.54 ? C22 L1P 260 A 1 HETATM 23 C C23 L1P . . . D 4 35.854 40.399 28.571 1 95.16 ? C23 L1P 260 A 1 HETATM 24 C C24 L1P . . . D 4 36.792 39.514 27.753 1 100 ? C24 L1P 260 A 1 HETATM 25 C C25 L1P . . . D 4 35.074 41.326 27.627 1 95.57 ? C25 L1P 260 A 1 HETATM 26 C C26 L1P . . . D 4 34.238 40.476 26.66 1 92.21 ? C26 L1P 260 A 1 HETATM 27 C C27 L1P . . . D 4 32.912 41.188 26.338 1 94.6 ? C27 L1P 260 A 1 HETATM 28 C C28 L1P . . . D 4 31.702 40.393 26.88 1 92.84 ? C28 L1P 260 A 1 HETATM 29 C C29 L1P . . . D 4 30.615 40.313 25.804 1 84.53 ? C29 L1P 260 A 1 HETATM 30 C C30 L1P . . . D 4 32.111 38.972 27.288 1 92.8 ? C30 L1P 260 A 1 HETATM 31 C C41 L1P . . . D 4 36.174 43.406 40.679 1 99.79 ? C41 L1P 260 A 1 HETATM 32 C C42 L1P . . . D 4 34.664 43.703 40.661 1 97.82 ? C42 L1P 260 A 1 HETATM 33 C C43 L1P . . . D 4 34.432 45.185 40.316 1 97.42 ? C43 L1P 260 A 1 HETATM 34 C C44 L1P . . . D 4 35.182 46.074 41.315 1 97.68 ? C44 L1P 260 A 1 HETATM 35 C C45 L1P . . . D 4 32.93 45.501 40.381 1 94.6 ? C45 L1P 260 A 1 HETATM 36 C C46 L1P . . . D 4 32.477 46.14 39.062 1 91.32 ? C46 L1P 260 A 1 HETATM 37 C C47 L1P . . . D 4 32.678 45.139 37.921 1 92.37 ? C47 L1P 260 A 1 HETATM 38 C C48 L1P . . . D 4 32.234 45.768 36.6 1 92.04 ? C48 L1P 260 A 1 HETATM 39 C C49 L1P . . . D 4 31.273 44.81 35.892 1 93.03 ? C49 L1P 260 A 1 HETATM 40 C C50 L1P . . . D 4 33.46 46.002 35.714 1 92.07 ? C50 L1P 260 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #