data_5K8K # _model_server_result.job_id 9OacYjFOJKMdkJ4aFHJl4g _model_server_result.datetime_utc '2024-10-23 12:29:55' _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 5k8k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5K8K # _exptl.entry_id 5K8K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 711.861 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE' _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 5K8K _cell.length_a 99.84 _cell.length_b 99.84 _cell.length_c 200.85 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K8K _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 C MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PHE 26 A PHE 26 1_555 A N MSE 27 A MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C MSE 27 A MSE 27 1_555 A N GLN 28 A GLN 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C ILE 172 A ILE 172 1_555 A N MSE 173 A MSE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C MSE 173 A MSE 173 1_555 A N ASP 174 A ASP 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C LYS 225 A LYS 225 1_555 A N MSE 226 A MSE 226 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C LYS 225 A LYS 225 1_555 A N MSE 226 A MSE 226 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 226 A MSE 226 1_555 A N ASP 227 A ASP 227 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 A C MSE 226 A MSE 226 1_555 A N ASP 227 A ASP 227 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASP 9 A ASP 9 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc2 A NE2 HIS 11 A HIS 11 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc3 A OD2 ASP 42 A ASP 42 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 A OD2 ASP 42 A ASP 42 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc5 A OD1 ASN 80 A ASN 80 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc6 A NE2 HIS 115 A HIS 115 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc7 A ND1 HIS 196 A HIS 196 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _chem_comp.formula 'C34 H66 N O12 P' _chem_comp.formula_weight 711.861 _chem_comp.id LP5 _chem_comp.mon_nstd_flag . _chem_comp.name '(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O48 P45 LP5 sing 213 n n O48 HO48 LP5 sing 214 n n P45 O1 LP5 sing 215 n n P45 O47 LP5 doub 216 n n P45 O46 LP5 sing 217 n n O46 HO46 LP5 sing 218 n n O1 C1 LP5 sing 219 n n C1 C2 LP5 sing 220 n n C1 O5 LP5 sing 221 n n C1 H1 LP5 sing 222 n n C2 C3 LP5 sing 223 n n C2 N2 LP5 sing 224 n n C2 H2 LP5 sing 225 n n N2 C7 LP5 sing 226 n n N2 HN2 LP5 sing 227 n n C7 O7 LP5 doub 228 n n C7 C8 LP5 sing 229 n n C8 C16 LP5 sing 230 n n C8 H81 LP5 sing 231 n n C8 H82 LP5 sing 232 n n C16 C17 LP5 sing 233 n n C16 O44 LP5 sing 234 n n C16 H16 LP5 sing 235 n n O44 HO44 LP5 sing 236 n n C17 C18 LP5 sing 237 n n C17 H171 LP5 sing 238 n n C17 H172 LP5 sing 239 n n C18 C19 LP5 sing 240 n n C18 H181 LP5 sing 241 n n C18 H182 LP5 sing 242 n n C19 C20 LP5 sing 243 n n C19 H191 LP5 sing 244 n n C19 H192 LP5 sing 245 n n C20 C21 LP5 sing 246 n n C20 H201 LP5 sing 247 n n C20 H202 LP5 sing 248 n n C21 C22 LP5 sing 249 n n C21 H211 LP5 sing 250 n n C21 H212 LP5 sing 251 n n C22 C23 LP5 sing 252 n n C22 H221 LP5 sing 253 n n C22 H222 LP5 sing 254 n n C23 C24 LP5 sing 255 n n C23 H231 LP5 sing 256 n n C23 H232 LP5 sing 257 n n C24 C25 LP5 sing 258 n n C24 H241 LP5 sing 259 n n C24 H242 LP5 sing 260 n n C25 C26 LP5 sing 261 n n C25 H251 LP5 sing 262 n n C25 H252 LP5 sing 263 n n C26 C27 LP5 sing 264 n n C26 H261 LP5 sing 265 n n C26 H262 LP5 sing 266 n n C27 H271 LP5 sing 267 n n C27 H272 LP5 sing 268 n n C27 H273 LP5 sing 269 n n C3 O3 LP5 sing 270 n n C3 C4 LP5 sing 271 n n C3 H3 LP5 sing 272 n n C4 O4 LP5 sing 273 n n C4 C5 LP5 sing 274 n n C4 H4 LP5 sing 275 n n C5 C6 LP5 sing 276 n n C5 O5 LP5 sing 277 n n C5 H5 LP5 sing 278 n n C6 O6 LP5 sing 279 n n C6 H61 LP5 sing 280 n n C6 H62 LP5 sing 281 n n O6 HO6 LP5 sing 282 n n O4 HO4 LP5 sing 283 n n O3 C28 LP5 sing 284 n n C28 C29 LP5 sing 285 n n C28 O42 LP5 doub 286 n n C29 C30 LP5 sing 287 n n C29 H291 LP5 sing 288 n n C29 H292 LP5 sing 289 n n C30 C31 LP5 sing 290 n n C30 O43 LP5 sing 291 n n C30 H30 LP5 sing 292 n n O43 HO43 LP5 sing 293 n n C31 C32 LP5 sing 294 n n C31 H311 LP5 sing 295 n n C31 H312 LP5 sing 296 n n C32 C33 LP5 sing 297 n n C32 H321 LP5 sing 298 n n C32 H322 LP5 sing 299 n n C33 C34 LP5 sing 300 n n C33 H331 LP5 sing 301 n n C33 H332 LP5 sing 302 n n C34 C35 LP5 sing 303 n n C34 H341 LP5 sing 304 n n C34 H342 LP5 sing 305 n n C35 C36 LP5 sing 306 n n C35 H351 LP5 sing 307 n n C35 H352 LP5 sing 308 n n C36 C37 LP5 sing 309 n n C36 H361 LP5 sing 310 n n C36 H362 LP5 sing 311 n n C37 C38 LP5 sing 312 n n C37 H371 LP5 sing 313 n n C37 H372 LP5 sing 314 n n C38 C39 LP5 sing 315 n n C38 H381 LP5 sing 316 n n C38 H382 LP5 sing 317 n n C39 C40 LP5 sing 318 n n C39 H391 LP5 sing 319 n n C39 H392 LP5 sing 320 n n C40 C41 LP5 sing 321 n n C40 H401 LP5 sing 322 n n C40 H402 LP5 sing 323 n n C41 H411 LP5 sing 324 n n C41 H412 LP5 sing 325 n n C41 H413 LP5 sing 326 n n # _atom_sites.entry_id 5K8K _atom_sites.fract_transf_matrix[1][1] 0.010016 _atom_sites.fract_transf_matrix[1][2] 0.005783 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011566 _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] 0.004979 _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 MN A 1 301 301 MN MN . C 2 MN A 1 302 302 MN MN . D 3 LP5 A 1 303 303 LP5 LP5 . E 4 ACT A 1 304 304 ACT ACT . F 4 ACT A 1 305 305 ACT ACT . G 5 GOL A 1 306 306 GOL GOL . H 5 GOL A 1 307 307 GOL GOL . I 6 HOH A 1 401 401 HOH HOH . I 6 HOH A 2 402 402 HOH HOH . I 6 HOH A 3 403 403 HOH HOH . I 6 HOH A 4 404 404 HOH HOH . I 6 HOH A 5 405 405 HOH HOH . I 6 HOH A 6 406 406 HOH HOH . I 6 HOH A 7 407 407 HOH HOH . I 6 HOH A 8 408 408 HOH HOH . I 6 HOH A 9 409 409 HOH HOH . I 6 HOH A 10 410 410 HOH HOH . I 6 HOH A 11 411 411 HOH HOH . I 6 HOH A 12 412 412 HOH HOH . I 6 HOH A 13 413 413 HOH HOH . I 6 HOH A 14 414 414 HOH HOH . I 6 HOH A 15 415 415 HOH HOH . I 6 HOH A 16 416 416 HOH HOH . I 6 HOH A 17 417 417 HOH HOH . I 6 HOH A 18 418 418 HOH HOH . I 6 HOH A 19 419 419 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 O O48 LP5 . . . D 3 3.56 25.924 10.766 1 65.96 ? O48 LP5 303 A 1 HETATM 2 P P45 LP5 . . . D 3 4.146 24.625 11.265 1 62.08 ? P45 LP5 303 A 1 HETATM 3 O O46 LP5 . . . D 3 5.527 24.898 11.804 1 66.49 ? O46 LP5 303 A 1 HETATM 4 O O47 LP5 . . . D 3 3.285 24.007 12.342 1 61.15 ? O47 LP5 303 A 1 HETATM 5 O O1 LP5 . . . D 3 4.186 23.556 10.019 1 60.52 ? O1 LP5 303 A 1 HETATM 6 C C1 LP5 . . . D 3 3.003 23.365 9.358 1 57.79 ? C1 LP5 303 A 1 HETATM 7 C C2 LP5 . . . D 3 2.819 21.869 9.109 1 54.28 ? C2 LP5 303 A 1 HETATM 8 N N2 LP5 . . . D 3 2.973 21.138 10.393 1 51.22 ? N2 LP5 303 A 1 HETATM 9 C C7 LP5 . . . D 3 1.818 20.547 11.048 1 52.28 ? C7 LP5 303 A 1 HETATM 10 C C8 LP5 . . . D 3 1.986 19.777 12.357 1 50.81 ? C8 LP5 303 A 1 HETATM 11 C C16 LP5 . . . D 3 1.665 20.647 13.565 1 50.83 ? C16 LP5 303 A 1 HETATM 12 O O44 LP5 . . . D 3 2.691 21.582 13.757 1 52.22 ? O44 LP5 303 A 1 HETATM 13 C C17 LP5 . . . D 3 1.561 19.733 14.782 1 49.83 ? C17 LP5 303 A 1 HETATM 14 C C18 LP5 . . . D 3 0.535 20.284 15.764 1 53.73 ? C18 LP5 303 A 1 HETATM 15 C C19 LP5 . . . D 3 -0.488 19.198 16.085 1 53.6 ? C19 LP5 303 A 1 HETATM 16 C C20 LP5 . . . D 3 -0.129 18.575 17.429 1 56.61 ? C20 LP5 303 A 1 HETATM 17 C C21 LP5 . . . D 3 -1.318 17.77 17.951 1 57.45 ? C21 LP5 303 A 1 HETATM 18 C C22 LP5 . . . D 3 -1.807 16.829 16.856 1 56.29 ? C22 LP5 303 A 1 HETATM 19 C C23 LP5 . . . D 3 -2.992 16.023 17.378 1 54.08 ? C23 LP5 303 A 1 HETATM 20 C C24 LP5 . . . D 3 -3.126 14.752 16.545 1 50.89 ? C24 LP5 303 A 1 HETATM 21 C C25 LP5 . . . D 3 -4.586 14.317 16.579 1 50.82 ? C25 LP5 303 A 1 HETATM 22 C C26 LP5 . . . D 3 -4.82 13.196 15.571 1 50.35 ? C26 LP5 303 A 1 HETATM 23 C C27 LP5 . . . D 3 -6.323 13.013 15.398 1 52.04 ? C27 LP5 303 A 1 HETATM 24 O O7 LP5 . . . D 3 0.737 20.65 10.572 1 55.15 ? O7 LP5 303 A 1 HETATM 25 C C3 LP5 . . . D 3 3.808 21.364 8.11 1 56.52 ? C3 LP5 303 A 1 HETATM 26 C C4 LP5 . . . D 3 3.785 22.167 6.874 1 53.02 ? C4 LP5 303 A 1 HETATM 27 C C5 LP5 . . . D 3 4.073 23.639 7.191 1 56.54 ? C5 LP5 303 A 1 HETATM 28 O O5 LP5 . . . D 3 3.021 24.145 8.114 1 56.9 ? O5 LP5 303 A 1 HETATM 29 C C6 LP5 . . . D 3 4.005 24.463 5.954 1 60.22 ? C6 LP5 303 A 1 HETATM 30 O O6 LP5 . . . D 3 2.708 24.417 5.427 1 63 ? O6 LP5 303 A 1 HETATM 31 O O4 LP5 . . . D 3 4.802 21.63 6.011 1 46.3 ? O4 LP5 303 A 1 HETATM 32 O O3 LP5 . . . D 3 3.495 19.977 7.742 1 60.88 ? O3 LP5 303 A 1 HETATM 33 C C28 LP5 . . . D 3 4.394 19.011 8.207 1 62.9 ? C28 LP5 303 A 1 HETATM 34 O O42 LP5 . . . D 3 5.546 19.268 8.326 1 66.35 ? O42 LP5 303 A 1 HETATM 35 C C29 LP5 . . . D 3 3.891 17.613 8.561 1 64.14 ? C29 LP5 303 A 1 HETATM 36 C C30 LP5 . . . D 3 4.92 16.584 8.095 1 67.81 ? C30 LP5 303 A 1 HETATM 37 O O43 LP5 . . . D 3 5.268 16.843 6.76 1 70.41 ? O43 LP5 303 A 1 HETATM 38 C C31 LP5 . . . D 3 4.356 15.167 8.215 1 65.99 ? C31 LP5 303 A 1 HETATM 39 C C32 LP5 . . . D 3 3.758 14.961 9.605 1 67.12 ? C32 LP5 303 A 1 HETATM 40 C C33 LP5 . . . D 3 3.8 13.477 9.961 1 69.51 ? C33 LP5 303 A 1 HETATM 41 C C34 LP5 . . . D 3 3.843 13.307 11.48 1 72.45 ? C34 LP5 303 A 1 HETATM 42 C C35 LP5 . . . D 3 3.187 11.993 11.908 1 73.55 ? C35 LP5 303 A 1 HETATM 43 C C36 LP5 . . . D 3 2.116 11.574 10.903 1 75.38 ? C36 LP5 303 A 1 HETATM 44 C C37 LP5 . . . D 3 1.261 10.464 11.506 1 77.86 ? C37 LP5 303 A 1 HETATM 45 C C38 LP5 . . . D 3 -0.222 10.785 11.309 1 78.02 ? C38 LP5 303 A 1 HETATM 46 C C39 LP5 . . . D 3 -0.894 10.794 12.681 1 79.02 ? C39 LP5 303 A 1 HETATM 47 C C40 LP5 . . . D 3 -2.298 10.199 12.598 1 80.36 ? C40 LP5 303 A 1 HETATM 48 C C41 LP5 . . . D 3 -2.748 9.798 14.003 1 79.9 ? C41 LP5 303 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 48 #