data_3OV6 # _model_server_result.job_id dqlE4ZFWLz0LbsZ15mO7qw _model_server_result.datetime_utc '2025-07-14 08:55:43' _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 3ov6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1105}' # _entry.id 3OV6 # _exptl.entry_id 3OV6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 708.986 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose _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 90 _cell.entry_id 3OV6 _cell.length_a 53.724 _cell.length_b 87.087 _cell.length_c 88.808 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OV6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 4 _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 disulf ? disulf1 A SG CYS 219 A CYS 102 1_555 A SG CYS 284 A CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 324 A CYS 207 1_555 A SG CYS 379 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? disulf ? disulf3 A SG CYS 28 A CYS 1025 1_555 A SG CYS 83 A CYS 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? covale ? covale1 B C1 NAG . A NAG 1 1_555 A ND2 ASN 137 A ASN 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.662 ? # _chem_comp.formula 'C38 H77 O9 P' _chem_comp.formula_weight 708.986 _chem_comp.id MK0 _chem_comp.mon_nstd_flag . _chem_comp.name 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose _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 C1 O1 MK0 sing 274 n n C1 C2 MK0 sing 275 n n C1 O5 MK0 sing 276 n n C1 H1 MK0 sing 277 n n O1 PBV MK0 sing 278 n n C2 O2 MK0 sing 279 n n C2 C3 MK0 sing 280 n n C2 H2 MK0 sing 281 n n O2 HO2 MK0 sing 282 n n C3 O3 MK0 sing 283 n n C3 C4 MK0 sing 284 n n C3 H3 MK0 sing 285 n n O3 HO3 MK0 sing 286 n n C4 O4 MK0 sing 287 n n C4 C5 MK0 sing 288 n n C4 H4 MK0 sing 289 n n O4 HO4 MK0 sing 290 n n C5 O5 MK0 sing 291 n n C5 C6 MK0 sing 292 n n C5 H5 MK0 sing 293 n n C6 O6 MK0 sing 294 n n C6 H6 MK0 sing 295 n n C6 H6A MK0 sing 296 n n O6 HO6 MK0 sing 297 n n CAA CAM MK0 sing 298 n n CAA HAA MK0 sing 299 n n CAA HAAA MK0 sing 300 n n CAA HAAB MK0 sing 301 n n CAB CBL MK0 sing 302 n n CAB HAB MK0 sing 303 n n CAB HABA MK0 sing 304 n n CAB HABB MK0 sing 305 n n CAC CBM MK0 sing 306 n n CAC HAC MK0 sing 307 n n CAC HACA MK0 sing 308 n n CAC HACB MK0 sing 309 n n CAD CBN MK0 sing 310 n n CAD HAD MK0 sing 311 n n CAD HADA MK0 sing 312 n n CAD HADB MK0 sing 313 n n CAE CBO MK0 sing 314 n n CAE HAE MK0 sing 315 n n CAE HAEA MK0 sing 316 n n CAE HAEB MK0 sing 317 n n CAF CBP MK0 sing 318 n n CAF HAF MK0 sing 319 n n CAF HAFA MK0 sing 320 n n CAF HAFB MK0 sing 321 n n OAG PBV MK0 sing 322 n n OAL PBV MK0 doub 323 n n CAM CAN MK0 sing 324 n n CAM HAM MK0 sing 325 n n CAM HAMA MK0 sing 326 n n CAN CAO MK0 sing 327 n n CAN HAN MK0 sing 328 n n CAN HANA MK0 sing 329 n n CAO CAP MK0 sing 330 n n CAO HAO MK0 sing 331 n n CAO HAOA MK0 sing 332 n n CAP CAQ MK0 sing 333 n n CAP HAP MK0 sing 334 n n CAP HAPA MK0 sing 335 n n CAQ CAY MK0 sing 336 n n CAQ HAQ MK0 sing 337 n n CAQ HAQA MK0 sing 338 n n CAR CAX MK0 sing 339 n n CAR CAZ MK0 sing 340 n n CAR HAR MK0 sing 341 n n CAR HARA MK0 sing 342 n n CAS CBA MK0 sing 343 n n CAS CBC MK0 sing 344 n n CAS HAS MK0 sing 345 n n CAS HASA MK0 sing 346 n n CAT CBB MK0 sing 347 n n CAT CBD MK0 sing 348 n n CAT HAT MK0 sing 349 n n CAT HATA MK0 sing 350 n n CAU CBE MK0 sing 351 n n CAU CBG MK0 sing 352 n n CAU HAU MK0 sing 353 n n CAU HAUA MK0 sing 354 n n CAV CBF MK0 sing 355 n n CAV CBH MK0 sing 356 n n CAV HAV MK0 sing 357 n n CAV HAVA MK0 sing 358 n n CAX OBI MK0 sing 359 n n CAX HAX MK0 sing 360 n n CAX HAXA MK0 sing 361 n n CAY CBL MK0 sing 362 n n CAY HAY MK0 sing 363 n n CAY HAYA MK0 sing 364 n n CAZ CBM MK0 sing 365 n n CAZ HAZ MK0 sing 366 n n CAZ HAZA MK0 sing 367 n n CBA CBL MK0 sing 368 n n CBA HBA MK0 sing 369 n n CBA HBAA MK0 sing 370 n n CBB CBM MK0 sing 371 n n CBB HBB MK0 sing 372 n n CBB HBBA MK0 sing 373 n n CBC CBN MK0 sing 374 n n CBC HBC MK0 sing 375 n n CBC HBCA MK0 sing 376 n n CBD CBO MK0 sing 377 n n CBD HBD MK0 sing 378 n n CBD HBDA MK0 sing 379 n n CBE CBN MK0 sing 380 n n CBE HBE MK0 sing 381 n n CBE HBEA MK0 sing 382 n n CBF CBO MK0 sing 383 n n CBF HBF MK0 sing 384 n n CBF HBFA MK0 sing 385 n n CBG CBP MK0 sing 386 n n CBG HBG MK0 sing 387 n n CBG HBGA MK0 sing 388 n n CBH CBP MK0 sing 389 n n CBH HBH MK0 sing 390 n n CBH HBHA MK0 sing 391 n n OBI PBV MK0 sing 392 n n CBL HBL MK0 sing 393 n n CBM HBM MK0 sing 394 n n CBN HBN MK0 sing 395 n n CBO HBO MK0 sing 396 n n CBP HBP MK0 sing 397 n n OAG H77 MK0 sing 398 n n # _atom_sites.entry_id 3OV6 _atom_sites.fract_transf_matrix[1][1] 0.018614 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011483 _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] 0.01126 _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 NAG A 1 1 1 NAG NAG . C 3 D12 A 1 1104 1 D12 D12 . D 4 MK0 A 1 1105 1 MK0 MK0 . E 5 HOH A 1 2 2 HOH HOH . E 5 HOH A 2 3 3 HOH HOH . E 5 HOH A 3 4 4 HOH HOH . E 5 HOH A 4 5 5 HOH HOH . E 5 HOH A 5 1106 1 HOH HOH . E 5 HOH A 6 1107 6 HOH HOH . E 5 HOH A 7 1108 7 HOH HOH . E 5 HOH A 8 1109 8 HOH HOH . E 5 HOH A 9 1110 9 HOH HOH . E 5 HOH A 10 1111 10 HOH HOH . E 5 HOH A 11 1112 11 HOH HOH . E 5 HOH A 12 1113 12 HOH HOH . E 5 HOH A 13 1114 13 HOH HOH . E 5 HOH A 14 1115 14 HOH HOH . E 5 HOH A 15 1116 15 HOH HOH . E 5 HOH A 16 1117 16 HOH HOH . E 5 HOH A 17 1118 17 HOH HOH . E 5 HOH A 18 1119 18 HOH HOH . E 5 HOH A 19 1120 19 HOH HOH . E 5 HOH A 20 1121 20 HOH HOH . E 5 HOH A 21 1122 21 HOH HOH . E 5 HOH A 22 1123 22 HOH HOH . E 5 HOH A 23 1124 23 HOH HOH . E 5 HOH A 24 1125 24 HOH HOH . E 5 HOH A 25 1126 25 HOH HOH . E 5 HOH A 26 1127 26 HOH HOH . E 5 HOH A 27 1128 27 HOH HOH . E 5 HOH A 28 1129 28 HOH HOH . E 5 HOH A 29 1130 29 HOH HOH . E 5 HOH A 30 1131 30 HOH HOH . E 5 HOH A 31 1132 31 HOH HOH . E 5 HOH A 32 1133 32 HOH HOH . E 5 HOH A 33 1134 33 HOH HOH . E 5 HOH A 34 1135 34 HOH HOH . E 5 HOH A 35 1136 35 HOH HOH . E 5 HOH A 36 1137 36 HOH HOH . E 5 HOH A 37 1138 37 HOH HOH . E 5 HOH A 38 1139 38 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 MK0 . . . D 4 -4.198 31.164 -40.596 1 108.21 ? C1 MK0 1105 A 1 HETATM 2 O O1 MK0 . . . D 4 -4.896 30.058 -41.168 1 115.22 ? O1 MK0 1105 A 1 HETATM 3 C C2 MK0 . . . D 4 -3.675 32.138 -41.666 1 112.13 ? C2 MK0 1105 A 1 HETATM 4 O O2 MK0 . . . D 4 -3.438 31.453 -42.88 1 114.57 ? O2 MK0 1105 A 1 HETATM 5 C C3 MK0 . . . D 4 -4.564 33.366 -41.945 1 116.27 ? C3 MK0 1105 A 1 HETATM 6 O O3 MK0 . . . D 4 -4.892 33.414 -43.325 1 113.02 ? O3 MK0 1105 A 1 HETATM 7 C C4 MK0 . . . D 4 -5.864 33.53 -41.14 1 114.25 ? C4 MK0 1105 A 1 HETATM 8 O O4 MK0 . . . D 4 -5.937 34.873 -40.677 1 107.6 ? O4 MK0 1105 A 1 HETATM 9 C C5 MK0 . . . D 4 -6.102 32.562 -39.969 1 107.79 ? C5 MK0 1105 A 1 HETATM 10 O O5 MK0 . . . D 4 -4.962 31.81 -39.585 1 103.31 ? O5 MK0 1105 A 1 HETATM 11 C C6 MK0 . . . D 4 -7.273 31.615 -40.259 1 107.03 ? C6 MK0 1105 A 1 HETATM 12 O O6 MK0 . . . D 4 -7.294 30.564 -39.312 1 96.45 ? O6 MK0 1105 A 1 HETATM 13 C CAA MK0 . . . D 4 -5.887 30.535 -26.237 1 42.86 ? CAA MK0 1105 A 1 HETATM 14 C CAB MK0 . . . D 4 -2.504 23.179 -25.095 1 51.22 ? CAB MK0 1105 A 1 HETATM 15 C CAC MK0 . . . D 4 -5.083 25.597 -36.309 1 69.9 ? CAC MK0 1105 A 1 HETATM 16 C CAD MK0 . . . D 4 -0.715 17.684 -29.586 1 54.27 ? CAD MK0 1105 A 1 HETATM 17 C CAE MK0 . . . D 4 -7.9 23.541 -31.751 1 64.03 ? CAE MK0 1105 A 1 HETATM 18 C CAF MK0 . . . D 4 -6.398 17.264 -31.549 1 63.48 ? CAF MK0 1105 A 1 HETATM 19 O OAG MK0 . . . D 4 -3.061 28.163 -40.953 1 110.21 ? OAG MK0 1105 A 1 HETATM 20 O OAL MK0 . . . D 4 -5.347 27.747 -42.021 1 101.53 ? OAL MK0 1105 A 1 HETATM 21 C CAM MK0 . . . D 4 -6.323 29.154 -26.652 1 53.44 ? CAM MK0 1105 A 1 HETATM 22 C CAN MK0 . . . D 4 -5.169 28.191 -26.905 1 57.06 ? CAN MK0 1105 A 1 HETATM 23 C CAO MK0 . . . D 4 -5.622 26.772 -27.026 1 55.02 ? CAO MK0 1105 A 1 HETATM 24 C CAP MK0 . . . D 4 -4.602 25.749 -27.479 1 57.95 ? CAP MK0 1105 A 1 HETATM 25 C CAQ MK0 . . . D 4 -4.393 24.61 -26.474 1 50.71 ? CAQ MK0 1105 A 1 HETATM 26 C CAR MK0 . . . D 4 -6.702 26.373 -38.595 1 83.99 ? CAR MK0 1105 A 1 HETATM 27 C CAS MK0 . . . D 4 -2.364 19.972 -27.218 1 54.98 ? CAS MK0 1105 A 1 HETATM 28 C CAT MK0 . . . D 4 -7.321 24.668 -34.519 1 73.5 ? CAT MK0 1105 A 1 HETATM 29 C CAU MK0 . . . D 4 -3.226 17.372 -31.216 1 55.74 ? CAU MK0 1105 A 1 HETATM 30 C CAV MK0 . . . D 4 -6.555 20.443 -32.328 1 64.61 ? CAV MK0 1105 A 1 HETATM 31 C CAX MK0 . . . D 4 -5.683 26.761 -39.659 1 88.59 ? CAX MK0 1105 A 1 HETATM 32 C CAY MK0 . . . D 4 -3.907 23.314 -27.098 1 58.8 ? CAY MK0 1105 A 1 HETATM 33 C CAZ MK0 . . . D 4 -6.521 24.914 -38.23 1 79.02 ? CAZ MK0 1105 A 1 HETATM 34 C CBA MK0 . . . D 4 -2.137 21.434 -26.769 1 54.61 ? CBA MK0 1105 A 1 HETATM 35 C CBB MK0 . . . D 4 -7.44 25.089 -35.969 1 73.08 ? CBB MK0 1105 A 1 HETATM 36 C CBC MK0 . . . D 4 -1.555 19.619 -28.471 1 55.31 ? CBC MK0 1105 A 1 HETATM 37 C CBD MK0 . . . D 4 -8.082 23.391 -34.222 1 67.03 ? CBD MK0 1105 A 1 HETATM 38 C CBE MK0 . . . D 4 -2.743 18.636 -30.541 1 64.96 ? CBE MK0 1105 A 1 HETATM 39 C CBF MK0 . . . D 4 -7.679 21.218 -32.979 1 65.34 ? CBF MK0 1105 A 1 HETATM 40 C CBG MK0 . . . D 4 -4.109 17.721 -32.405 1 58.03 ? CBG MK0 1105 A 1 HETATM 41 C CBH MK0 . . . D 4 -6.193 19.153 -33.038 1 59.53 ? CBH MK0 1105 A 1 HETATM 42 O OBI MK0 . . . D 4 -5.027 28.015 -39.53 1 94.2 ? OBI MK0 1105 A 1 HETATM 43 C CBL MK0 . . . D 4 -3.18 22.378 -26.152 1 52.4 ? CBL MK0 1105 A 1 HETATM 44 C CBM MK0 . . . D 4 -6.215 24.716 -36.767 1 74.74 ? CBM MK0 1105 A 1 HETATM 45 C CBN MK0 . . . D 4 -1.982 18.401 -29.243 1 60.93 ? CBN MK0 1105 A 1 HETATM 46 C CBO MK0 . . . D 4 -7.469 22.755 -32.999 1 69.89 ? CBO MK0 1105 A 1 HETATM 47 C CBP MK0 . . . D 4 -5.448 18.335 -32.006 1 61.05 ? CBP MK0 1105 A 1 HETATM 48 P PBV MK0 . . . D 4 -4.534 28.449 -40.978 1 120.32 ? PBV MK0 1105 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #