data_9CXD # _model_server_result.job_id 7vw_wpfUx9qDRER6LKDaOQ _model_server_result.datetime_utc '2025-07-04 18:23:05' _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 9cxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 9CXD # _exptl.entry_id 9CXD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 10 _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 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 9CXD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CXD _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 10 _struct_asym.id K _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 7 oligosaccharide 8 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 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 8 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 8 3 2 BMA NAG C1 O1 . O4 HO4 . 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 7 n H NAG 1 F 1 NAG A 551 NAG 7 n H NAG 2 F 2 NAG A 553 NAG 8 n I NAG 1 G 1 NAG F 1 NAG 8 n I NAG 2 G 2 NAG F 2 NAG 8 n I BMA 3 G 3 BMA F 3 BMA # 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 135 A CYS 136 1_555 A SG CYS 149 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 139 B CYS 139 1_555 B SG CYS 153 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 136 C CYS 136 1_555 C SG CYS 150 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 D SG CYS 136 D CYS 136 1_555 D SG CYS 150 D CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 E SG CYS 151 E CYS 151 1_555 E SG CYS 165 E CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 F SG CYS 23 I CYS 23 1_555 F SG CYS 88 I CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 G SG CYS 22 J CYS 22 1_555 G SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 79 A ASN 80 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 148 A ASN 149 1_555 I C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 B ND2 ASN 111 B ASN 111 1_555 L C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 C ND2 ASN 149 C ASN 149 1_555 M C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 D ND2 ASN 149 D ASN 149 1_555 N C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 E ND2 ASN 208 E ASN 208 1_555 O C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 I O4 NAG . G NAG 1 1_555 I C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 I O4 NAG . G NAG 2 1_555 I C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 327 n n C1 C2 PIO sing 328 n n C1 C6 PIO sing 329 n n C1 H1 PIO sing 330 n n O1 P1 PIO sing 331 n n P1 O11 PIO sing 332 n n O11 H11 PIO sing 333 n n P1 O12 PIO doub 334 n n P1 O13 PIO sing 335 n n C2 O2 PIO sing 336 n n C2 C3 PIO sing 337 n n C2 H2 PIO sing 338 n n O2 HO2 PIO sing 339 n n C3 O3 PIO sing 340 n n C3 C4 PIO sing 341 n n C3 H3 PIO sing 342 n n O3 HO3 PIO sing 343 n n C4 O4 PIO sing 344 n n C4 C5 PIO sing 345 n n C4 H4 PIO sing 346 n n O4 P4 PIO sing 347 n n P4 O41 PIO sing 348 n n O41 H41 PIO sing 349 n n P4 O42 PIO doub 350 n n P4 O43 PIO sing 351 n n O43 H43 PIO sing 352 n n C5 O5 PIO sing 353 n n C5 C6 PIO sing 354 n n C5 H5 PIO sing 355 n n O5 P5 PIO sing 356 n n P5 O51 PIO sing 357 n n O51 H51 PIO sing 358 n n P5 O52 PIO sing 359 n n O52 H52 PIO sing 360 n n P5 O53 PIO doub 361 n n C6 O6 PIO sing 362 n n C6 H6 PIO sing 363 n n O6 HO6 PIO sing 364 n n O13 C1C PIO sing 365 n n C1A O1A PIO doub 366 n n C1A C2A PIO sing 367 n n C1A O2C PIO sing 368 n n C1B O1B PIO doub 369 n n C1B C2B PIO sing 370 n n C1B O3C PIO sing 371 n n C1C C2C PIO sing 372 n n C1C H1C PIO sing 373 n n C1C H1CA PIO sing 374 n n C2A C3A PIO sing 375 n n C2A H2A PIO sing 376 n n C2A H2AA PIO sing 377 n n C2B C3B PIO sing 378 n n C2B H2B PIO sing 379 n n C2B H2BA PIO sing 380 n n C2C O2C PIO sing 381 n n C2C C3C PIO sing 382 n n C2C H2C PIO sing 383 n n C3A C4A PIO sing 384 n n C3A H3A PIO sing 385 n n C3A H3AA PIO sing 386 n n C3B C4B PIO sing 387 n n C3B H3B PIO sing 388 n n C3B H3BA PIO sing 389 n n C3C O3C PIO sing 390 n n C3C H3C PIO sing 391 n n C3C H3CA PIO sing 392 n n C4A C5A PIO sing 393 n n C4A H4A PIO sing 394 n n C4A H4AA PIO sing 395 n n C4B C5B PIO sing 396 n n C4B H4B PIO sing 397 n n C4B H4BA PIO sing 398 n n C5A C6A PIO sing 399 n n C5A H5A PIO sing 400 n n C5A H5AA PIO sing 401 n n C5B C6B PIO sing 402 n n C5B H5B PIO sing 403 n n C5B H5BA PIO sing 404 n n C6A C7A PIO sing 405 n n C6A H6A PIO sing 406 n n C6A H6AA PIO sing 407 n n C6B C7B PIO sing 408 n n C6B H6B PIO sing 409 n n C6B H6BA PIO sing 410 n n C7A C8A PIO sing 411 n n C7A H7A PIO sing 412 n n C7A H7AA PIO sing 413 n n C7B C8B PIO sing 414 n n C7B H7B PIO sing 415 n n C7B H7BA PIO sing 416 n n C8A H8A PIO sing 417 n n C8A H8AA PIO sing 418 n n C8A H8AB PIO sing 419 n n C8B H8B PIO sing 420 n n C8B H8BA PIO sing 421 n n C8B H8BB PIO sing 422 n n # _atom_sites.entry_id 9CXD _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 J 9 ABU A 1 501 552 ABU ABU . K 10 PIO B 1 501 501 PIO PIO . L 11 NAG B 1 502 601 NAG NAG . M 11 NAG C 1 501 1 NAG NAG . N 11 NAG D 1 501 562 NAG NAG . O 11 NAG E 1 501 436 NAG NAG . # 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 PIO . . . K 10 119.007 97.138 164.649 1 251.16 ? C1 PIO 501 B 1 HETATM 2 O O1 PIO . . . K 10 118.654 97.328 163.264 1 252.44 ? O1 PIO 501 B 1 HETATM 3 P P1 PIO . . . K 10 119.743 97.041 162.095 1 258.89 ? P1 PIO 501 B 1 HETATM 4 C C2 PIO . . . K 10 118.158 96.01 165.219 1 250.86 ? C2 PIO 501 B 1 HETATM 5 O O2 PIO . . . K 10 116.775 96.312 165.063 1 250.74 ? O2 PIO 501 B 1 HETATM 6 C C3 PIO . . . K 10 118.486 95.797 166.692 1 253.27 ? C3 PIO 501 B 1 HETATM 7 O O3 PIO . . . K 10 117.665 94.765 167.23 1 253.5 ? O3 PIO 501 B 1 HETATM 8 C C4 PIO . . . K 10 118.284 97.09 167.471 1 254.51 ? C4 PIO 501 B 1 HETATM 9 O O4 PIO . . . K 10 118.717 96.885 168.832 1 253.67 ? O4 PIO 501 B 1 HETATM 10 P P4 PIO . . . K 10 117.66 96.567 170.026 1 255.53 ? P4 PIO 501 B 1 HETATM 11 C C5 PIO . . . K 10 119.086 98.235 166.873 1 254.97 ? C5 PIO 501 B 1 HETATM 12 O O5 PIO . . . K 10 118.762 99.443 167.593 1 254.93 ? O5 PIO 501 B 1 HETATM 13 P P5 PIO . . . K 10 119.858 100.6 167.915 1 257.68 ? P5 PIO 501 B 1 HETATM 14 C C6 PIO . . . K 10 118.762 98.442 165.398 1 253.72 ? C6 PIO 501 B 1 HETATM 15 O O6 PIO . . . K 10 119.584 99.469 164.854 1 253.91 ? O6 PIO 501 B 1 HETATM 16 O O11 PIO . . . K 10 119.557 97.964 160.951 1 254.94 ? O11 PIO 501 B 1 HETATM 17 O O12 PIO . . . K 10 121.101 96.852 162.645 1 253.5 ? O12 PIO 501 B 1 HETATM 18 O O13 PIO . . . K 10 119.212 95.596 161.674 1 255.72 ? O13 PIO 501 B 1 HETATM 19 C C1A PIO . . . K 10 118.923 92.174 160.406 1 252.96 ? C1A PIO 501 B 1 HETATM 20 O O1A PIO . . . K 10 118.743 91.458 161.355 1 250.56 ? O1A PIO 501 B 1 HETATM 21 C C1B PIO . . . K 10 114.794 93.364 159.115 1 252.56 ? C1B PIO 501 B 1 HETATM 22 O O1B PIO . . . K 10 113.809 93.657 159.737 1 250.73 ? O1B PIO 501 B 1 HETATM 23 C C1C PIO . . . K 10 117.797 95.367 161.511 1 253.29 ? C1C PIO 501 B 1 HETATM 24 C C2A PIO . . . K 10 119.764 91.826 159.213 1 253.52 ? C2A PIO 501 B 1 HETATM 25 C C2B PIO . . . K 10 114.817 93.039 157.649 1 252.8 ? C2B PIO 501 B 1 HETATM 26 C C2C PIO . . . K 10 117.56 93.886 161.384 1 252.82 ? C2C PIO 501 B 1 HETATM 27 O O2C PIO . . . K 10 118.388 93.398 160.284 1 254.28 ? O2C PIO 501 B 1 HETATM 28 C C3A PIO . . . K 10 119.102 92.171 157.886 1 253.03 ? C3A PIO 501 B 1 HETATM 29 C C3B PIO . . . K 10 115.606 94.045 156.821 1 252.61 ? C3B PIO 501 B 1 HETATM 30 C C3C PIO . . . K 10 116.122 93.574 161.064 1 251.16 ? C3C PIO 501 B 1 HETATM 31 O O3C PIO . . . K 10 116.013 93.286 159.652 1 253.03 ? O3C PIO 501 B 1 HETATM 32 O O41 PIO . . . K 10 116.288 96.62 169.387 1 253.93 ? O41 PIO 501 B 1 HETATM 33 O O42 PIO . . . K 10 118.023 95.191 170.536 1 253.38 ? O42 PIO 501 B 1 HETATM 34 O O43 PIO . . . K 10 117.867 97.656 171.059 1 251.81 ? O43 PIO 501 B 1 HETATM 35 C C4A PIO . . . K 10 120.021 91.956 156.693 1 252.04 ? C4A PIO 501 B 1 HETATM 36 C C4B PIO . . . K 10 115.622 93.714 155.336 1 250.86 ? C4B PIO 501 B 1 HETATM 37 O O51 PIO . . . K 10 119.779 101.571 166.756 1 253.9 ? O51 PIO 501 B 1 HETATM 38 O O52 PIO . . . K 10 121.196 99.893 167.996 1 254.66 ? O52 PIO 501 B 1 HETATM 39 O O53 PIO . . . K 10 119.435 101.215 169.23 1 252.71 ? O53 PIO 501 B 1 HETATM 40 C C5A PIO . . . K 10 119.392 92.314 155.357 1 252.67 ? C5A PIO 501 B 1 HETATM 41 C C5B PIO . . . K 10 116.443 94.683 154.501 1 251.36 ? C5B PIO 501 B 1 HETATM 42 C C6A PIO . . . K 10 120.341 92.186 154.175 1 251.79 ? C6A PIO 501 B 1 HETATM 43 C C6B PIO . . . K 10 116.436 94.38 153.011 1 251.22 ? C6B PIO 501 B 1 HETATM 44 C C7A PIO . . . K 10 119.722 92.568 152.84 1 251.65 ? C7A PIO 501 B 1 HETATM 45 C C7B PIO . . . K 10 117.264 95.352 152.184 1 249.93 ? C7B PIO 501 B 1 HETATM 46 C C8A PIO . . . K 10 120.691 92.465 151.683 1 250.86 ? C8A PIO 501 B 1 HETATM 47 C C8B PIO . . . K 10 117.233 95.049 150.702 1 248.78 ? C8B PIO 501 B 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 47 #