data_9BU2 # _model_server_result.job_id l5nsc6G6DdvpL8biCgqL7Q _model_server_result.datetime_utc '2024-11-19 20:55:35' _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 9bu2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":504}' # _entry.id 9BU2 # _exptl.entry_id 9BU2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _entity.pdbx_number_of_molecules 25 _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 9BU2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BU2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 U N N ? 4 W N N ? 4 X N N ? 4 Y N N ? 4 Z N N ? 4 EA N N ? 4 GA N N ? 4 HA N N ? 4 IA N N ? 4 JA N N ? 4 OA N N ? 4 QA N N ? 4 RA N N ? 4 SA N N ? 4 TA N N ? 4 YA N N ? 4 CB N N ? 4 DB N N ? 4 EB N N ? 4 FB N N ? 4 GB N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 F NAG 1 F 1 NAG A 502 NAG 2 n F NAG 2 F 2 NAG A 503 NAG 2 n G NAG 1 G 1 NAG B 502 NAG 2 n G NAG 2 G 2 NAG B 503 NAG 2 n H NAG 1 H 1 NAG C 502 NAG 2 n H NAG 2 H 2 NAG C 503 NAG 2 n I NAG 1 I 1 NAG D 502 NAG 2 n I NAG 2 I 2 NAG D 503 NAG 2 n J NAG 1 J 1 NAG E 502 NAG 2 n J NAG 2 J 2 NAG E 503 NAG # 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 231 A CYS 198 1_555 A SG CYS 242 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 231 B CYS 198 1_555 B SG CYS 242 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 C SG CYS 231 C CYS 198 1_555 C SG CYS 242 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 D SG CYS 231 D CYS 198 1_555 D SG CYS 242 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 E SG CYS 231 E CYS 198 1_555 E SG CYS 242 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 71 A ASN 38 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 B ND2 ASN 71 B ASN 38 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C ND2 ASN 71 C ASN 38 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 D ND2 ASN 71 D ASN 38 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 E ND2 ASN 71 E ASN 38 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C25 H49 O19 P3' _chem_comp.formula_weight 746.566 _chem_comp.id PIO _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' # 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 PIO sing 290 n n C1 C2 PIO sing 291 n n C1 C6 PIO sing 292 n n C1 H1 PIO sing 293 n n O1 P1 PIO sing 294 n n P1 O11 PIO sing 295 n n O11 H11 PIO sing 296 n n P1 O12 PIO doub 297 n n P1 O13 PIO sing 298 n n C2 O2 PIO sing 299 n n C2 C3 PIO sing 300 n n C2 H2 PIO sing 301 n n O2 HO2 PIO sing 302 n n C3 O3 PIO sing 303 n n C3 C4 PIO sing 304 n n C3 H3 PIO sing 305 n n O3 HO3 PIO sing 306 n n C4 O4 PIO sing 307 n n C4 C5 PIO sing 308 n n C4 H4 PIO sing 309 n n O4 P4 PIO sing 310 n n P4 O41 PIO sing 311 n n O41 H41 PIO sing 312 n n P4 O42 PIO doub 313 n n P4 O43 PIO sing 314 n n O43 H43 PIO sing 315 n n C5 O5 PIO sing 316 n n C5 C6 PIO sing 317 n n C5 H5 PIO sing 318 n n O5 P5 PIO sing 319 n n P5 O51 PIO sing 320 n n O51 H51 PIO sing 321 n n P5 O52 PIO sing 322 n n O52 H52 PIO sing 323 n n P5 O53 PIO doub 324 n n C6 O6 PIO sing 325 n n C6 H6 PIO sing 326 n n O6 HO6 PIO sing 327 n n O13 C1C PIO sing 328 n n C1A O1A PIO doub 329 n n C1A C2A PIO sing 330 n n C1A O2C PIO sing 331 n n C1B O1B PIO doub 332 n n C1B C2B PIO sing 333 n n C1B O3C PIO sing 334 n n C1C C2C PIO sing 335 n n C1C H1C PIO sing 336 n n C1C H1CA PIO sing 337 n n C2A C3A PIO sing 338 n n C2A H2A PIO sing 339 n n C2A H2AA PIO sing 340 n n C2B C3B PIO sing 341 n n C2B H2B PIO sing 342 n n C2B H2BA PIO sing 343 n n C2C O2C PIO sing 344 n n C2C C3C PIO sing 345 n n C2C H2C PIO sing 346 n n C3A C4A PIO sing 347 n n C3A H3A PIO sing 348 n n C3A H3AA PIO sing 349 n n C3B C4B PIO sing 350 n n C3B H3B PIO sing 351 n n C3B H3BA PIO sing 352 n n C3C O3C PIO sing 353 n n C3C H3C PIO sing 354 n n C3C H3CA PIO sing 355 n n C4A C5A PIO sing 356 n n C4A H4A PIO sing 357 n n C4A H4AA PIO sing 358 n n C4B C5B PIO sing 359 n n C4B H4B PIO sing 360 n n C4B H4BA PIO sing 361 n n C5A C6A PIO sing 362 n n C5A H5A PIO sing 363 n n C5A H5AA PIO sing 364 n n C5B C6B PIO sing 365 n n C5B H5B PIO sing 366 n n C5B H5BA PIO sing 367 n n C6A C7A PIO sing 368 n n C6A H6A PIO sing 369 n n C6A H6AA PIO sing 370 n n C6B C7B PIO sing 371 n n C6B H6B PIO sing 372 n n C6B H6BA PIO sing 373 n n C7A C8A PIO sing 374 n n C7A H7A PIO sing 375 n n C7A H7AA PIO sing 376 n n C7B C8B PIO sing 377 n n C7B H7B PIO sing 378 n n C7B H7BA PIO sing 379 n n C8A H8A PIO sing 380 n n C8A H8AA PIO sing 381 n n C8A H8AB PIO sing 382 n n C8B H8B PIO sing 383 n n C8B H8BA PIO sing 384 n n C8B H8BB PIO sing 385 n n # _atom_sites.entry_id 9BU2 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 K 3 GLY A 1 501 501 GLY GLY . L 3 GLY A 1 502 501 GLY GLY . M 4 PIO A 1 503 504 PIO PIO . N 4 PIO A 1 504 506 PIO PIO . O 4 PIO A 1 505 507 PIO PIO . P 4 PIO A 1 506 508 PIO PIO . Q 5 PX4 A 1 507 509 PX4 PX4 . R 5 PX4 A 1 508 513 PX4 PX4 . S 5 PX4 A 1 509 514 PX4 PX4 . T 5 PX4 A 1 510 515 PX4 PX4 . U 4 PIO A 1 511 505 PIO PIO . V 3 GLY B 1 501 501 GLY GLY . W 4 PIO B 1 502 504 PIO PIO . X 4 PIO B 1 503 506 PIO PIO . Y 4 PIO B 1 504 507 PIO PIO . Z 4 PIO B 1 505 508 PIO PIO . AA 5 PX4 B 1 506 509 PX4 PX4 . BA 5 PX4 B 1 507 513 PX4 PX4 . CA 5 PX4 B 1 508 514 PX4 PX4 . DA 5 PX4 B 1 509 515 PX4 PX4 . EA 4 PIO B 1 510 505 PIO PIO . FA 3 GLY C 1 501 501 GLY GLY . GA 4 PIO C 1 502 504 PIO PIO . HA 4 PIO C 1 503 506 PIO PIO . IA 4 PIO C 1 504 507 PIO PIO . JA 4 PIO C 1 505 508 PIO PIO . KA 5 PX4 C 1 506 509 PX4 PX4 . LA 5 PX4 C 1 507 513 PX4 PX4 . MA 5 PX4 C 1 508 514 PX4 PX4 . NA 5 PX4 C 1 509 515 PX4 PX4 . OA 4 PIO C 1 510 505 PIO PIO . PA 3 GLY D 1 501 501 GLY GLY . QA 4 PIO D 1 502 504 PIO PIO . RA 4 PIO D 1 503 506 PIO PIO . SA 4 PIO D 1 504 507 PIO PIO . TA 4 PIO D 1 505 508 PIO PIO . UA 5 PX4 D 1 506 509 PX4 PX4 . VA 5 PX4 D 1 507 513 PX4 PX4 . WA 5 PX4 D 1 508 514 PX4 PX4 . XA 5 PX4 D 1 509 515 PX4 PX4 . YA 4 PIO D 1 510 505 PIO PIO . ZA 5 PX4 E 1 501 513 PX4 PX4 . AB 5 PX4 E 1 502 514 PX4 PX4 . BB 5 PX4 E 1 503 515 PX4 PX4 . CB 4 PIO E 1 504 505 PIO PIO . DB 4 PIO E 1 505 504 PIO PIO . EB 4 PIO E 1 506 506 PIO PIO . FB 4 PIO E 1 507 507 PIO PIO . GB 4 PIO E 1 508 508 PIO PIO . HB 5 PX4 E 1 509 509 PX4 PX4 . IB 6 HOH A 1 601 504 HOH HOH . JB 6 HOH B 1 601 504 HOH HOH . KB 6 HOH C 1 601 504 HOH HOH . LB 6 HOH D 1 601 504 HOH HOH . MB 6 HOH E 1 601 504 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 C1A PIO . . . N 4 143.929 106.939 128.507 1 134.55 ? C1A PIO 504 A 1 HETATM 2 O O1A PIO . . . N 4 143.446 106.492 129.516 1 134.55 ? O1A PIO 504 A 1 HETATM 3 C C2A PIO . . . N 4 143.36 108.054 127.663 1 134.55 ? C2A PIO 504 A 1 HETATM 4 O O2C PIO . . . N 4 145.083 106.448 128.019 1 134.55 ? O2C PIO 504 A 1 HETATM 5 C C3A PIO . . . N 4 143.77 108.014 126.219 1 134.55 ? C3A PIO 504 A 1 HETATM 6 C C4A PIO . . . N 4 142.926 108.927 125.346 1 134.55 ? C4A PIO 504 A 1 HETATM 7 C C5A PIO . . . N 4 143.592 109.343 124.056 1 134.55 ? C5A PIO 504 A 1 HETATM 8 C C6A PIO . . . N 4 142.738 110.217 123.17 1 134.55 ? C6A PIO 504 A 1 HETATM 9 C C7A PIO . . . N 4 143.149 110.236 121.718 1 134.55 ? C7A PIO 504 A 1 HETATM 10 C C8A PIO . . . N 4 142.486 111.323 120.907 1 134.55 ? C8A PIO 504 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 10 #