data_6W7E # _model_server_result.job_id 050rfqaik9LdqTWwFSjKXw _model_server_result.datetime_utc '2024-11-13 08:19:06' _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 6w7e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":407}' # _entry.id 6W7E # _exptl.entry_id 6W7E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 7 _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 6W7E _cell.length_a 67.368 _cell.length_b 122.534 _cell.length_c 126.552 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6W7E _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 7 _struct_asym.id I _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 74 A CYS 93 1_555 B SG CYS 74 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A O THR 123 A THR 142 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc2 A O THR 123 A THR 142 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc3 A OG1 THR 123 A THR 142 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.284 ? metalc ? metalc4 A O ILE 124 A ILE 143 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc5 A O THR 232 A THR 251 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc6 A O THR 232 A THR 251 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc7 A OG1 THR 232 A THR 251 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.307 ? metalc ? metalc8 A O ILE 233 A ILE 252 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc9 H K K . A K 406 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc10 H K K . A K 406 1_555 B O ILE 124 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.001 ? metalc ? metalc11 H K K . A K 406 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc12 H K K . A K 406 1_555 B O ILE 233 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc13 B O THR 123 B THR 142 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc14 B OG1 THR 123 B THR 142 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.044 ? metalc ? metalc15 B O THR 232 B THR 251 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc16 B OG1 THR 232 B THR 251 1_555 P K K . B K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? # _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 373 n n C1 C2 PIO sing 374 n n C1 C6 PIO sing 375 n n C1 H1 PIO sing 376 n n O1 P1 PIO sing 377 n n P1 O11 PIO sing 378 n n O11 H11 PIO sing 379 n n P1 O12 PIO doub 380 n n P1 O13 PIO sing 381 n n C2 O2 PIO sing 382 n n C2 C3 PIO sing 383 n n C2 H2 PIO sing 384 n n O2 HO2 PIO sing 385 n n C3 O3 PIO sing 386 n n C3 C4 PIO sing 387 n n C3 H3 PIO sing 388 n n O3 HO3 PIO sing 389 n n C4 O4 PIO sing 390 n n C4 C5 PIO sing 391 n n C4 H4 PIO sing 392 n n O4 P4 PIO sing 393 n n P4 O41 PIO sing 394 n n O41 H41 PIO sing 395 n n P4 O42 PIO doub 396 n n P4 O43 PIO sing 397 n n O43 H43 PIO sing 398 n n C5 O5 PIO sing 399 n n C5 C6 PIO sing 400 n n C5 H5 PIO sing 401 n n O5 P5 PIO sing 402 n n P5 O51 PIO sing 403 n n O51 H51 PIO sing 404 n n P5 O52 PIO sing 405 n n O52 H52 PIO sing 406 n n P5 O53 PIO doub 407 n n C6 O6 PIO sing 408 n n C6 H6 PIO sing 409 n n O6 HO6 PIO sing 410 n n O13 C1C PIO sing 411 n n C1A O1A PIO doub 412 n n C1A C2A PIO sing 413 n n C1A O2C PIO sing 414 n n C1B O1B PIO doub 415 n n C1B C2B PIO sing 416 n n C1B O3C PIO sing 417 n n C1C C2C PIO sing 418 n n C1C H1C PIO sing 419 n n C1C H1CA PIO sing 420 n n C2A C3A PIO sing 421 n n C2A H2A PIO sing 422 n n C2A H2AA PIO sing 423 n n C2B C3B PIO sing 424 n n C2B H2B PIO sing 425 n n C2B H2BA PIO sing 426 n n C2C O2C PIO sing 427 n n C2C C3C PIO sing 428 n n C2C H2C PIO sing 429 n n C3A C4A PIO sing 430 n n C3A H3A PIO sing 431 n n C3A H3AA PIO sing 432 n n C3B C4B PIO sing 433 n n C3B H3B PIO sing 434 n n C3B H3BA PIO sing 435 n n C3C O3C PIO sing 436 n n C3C H3C PIO sing 437 n n C3C H3CA PIO sing 438 n n C4A C5A PIO sing 439 n n C4A H4A PIO sing 440 n n C4A H4AA PIO sing 441 n n C4B C5B PIO sing 442 n n C4B H4B PIO sing 443 n n C4B H4BA PIO sing 444 n n C5A C6A PIO sing 445 n n C5A H5A PIO sing 446 n n C5A H5AA PIO sing 447 n n C5B C6B PIO sing 448 n n C5B H5B PIO sing 449 n n C5B H5BA PIO sing 450 n n C6A C7A PIO sing 451 n n C6A H6A PIO sing 452 n n C6A H6AA PIO sing 453 n n C6B C7B PIO sing 454 n n C6B H6B PIO sing 455 n n C6B H6BA PIO sing 456 n n C7A C8A PIO sing 457 n n C7A H7A PIO sing 458 n n C7A H7AA PIO sing 459 n n C7B C8B PIO sing 460 n n C7B H7B PIO sing 461 n n C7B H7BA PIO sing 462 n n C8A H8A PIO sing 463 n n C8A H8AA PIO sing 464 n n C8A H8AB PIO sing 465 n n C8B H8B PIO sing 466 n n C8B H8BA PIO sing 467 n n C8B H8BB PIO sing 468 n n # _atom_sites.entry_id 6W7E _atom_sites.fract_transf_matrix[1][1] 0.014844 _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] 0.008161 _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] 0.007902 _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 2 CD A 1 401 1 CD CD . D 2 CD A 1 402 3 CD CD . E 3 1PE A 1 403 1 1PE 1PE . F 4 LNK A 1 404 2 LNK LNK . G 5 OCT A 1 405 2 OCT OCT . H 6 K A 1 406 2 K K . I 7 PIO A 1 407 1 PIO PIO . J 2 CD B 1 401 2 CD CD . K 2 CD B 1 402 4 CD CD . L 4 LNK B 1 403 1 LNK LNK . M 5 OCT B 1 404 1 OCT OCT . N 5 OCT B 1 405 3 OCT OCT . O 8 D12 B 1 406 1 D12 D12 . P 6 K B 1 407 1 K K . Q 9 R16 B 1 408 1 R16 R16 . # 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 . . . I 7 23.447 -10.858 -17.328 1 300 ? C1 PIO 407 A 1 HETATM 2 O O1 PIO . . . I 7 23.121 -12.118 -16.774 1 300 ? O1 PIO 407 A 1 HETATM 3 P P1 PIO . . . I 7 23.632 -12.436 -15.233 1 300 ? P1 PIO 407 A 1 HETATM 4 C C2 PIO . . . I 7 22.356 -9.84 -16.965 1 300 ? C2 PIO 407 A 1 HETATM 5 O O2 PIO . . . I 7 21.113 -10.283 -17.459 1 300 ? O2 PIO 407 A 1 HETATM 6 C C3 PIO . . . I 7 22.657 -8.437 -17.522 1 300 ? C3 PIO 407 A 1 HETATM 7 O O3 PIO . . . I 7 21.434 -7.795 -17.798 1 300 ? O3 PIO 407 A 1 HETATM 8 C C4 PIO . . . I 7 23.507 -8.431 -18.808 1 300 ? C4 PIO 407 A 1 HETATM 9 O O4 PIO . . . I 7 24.882 -8.311 -18.515 1 300 ? O4 PIO 407 A 1 HETATM 10 P P4 PIO . . . I 7 25.454 -7.239 -17.399 1 300 ? P4 PIO 407 A 1 HETATM 11 C C5 PIO . . . I 7 23.34 -9.708 -19.645 1 300 ? C5 PIO 407 A 1 HETATM 12 O O5 PIO . . . I 7 22.033 -9.793 -20.165 1 300 ? O5 PIO 407 A 1 HETATM 13 P P5 PIO . . . I 7 21.851 -9.726 -21.803 1 300 ? P5 PIO 407 A 1 HETATM 14 C C6 PIO . . . I 7 23.677 -10.979 -18.847 1 300 ? C6 PIO 407 A 1 HETATM 15 O O6 PIO . . . I 7 25.044 -11.235 -19.058 1 300 ? O6 PIO 407 A 1 HETATM 16 O O11 PIO . . . I 7 22.846 -11.589 -14.262 1 300 -1 O11 PIO 407 A 1 HETATM 17 O O12 PIO . . . I 7 25.1 -12.094 -15.117 1 300 ? O12 PIO 407 A 1 HETATM 18 O O13 PIO . . . I 7 23.407 -14.023 -14.849 1 300 ? O13 PIO 407 A 1 HETATM 19 C C1A PIO . . . I 7 23.702 -15.424 -10.3 1 278.84 ? C1A PIO 407 A 1 HETATM 20 O O1A PIO . . . I 7 22.756 -14.866 -9.843 1 275.52 ? O1A PIO 407 A 1 HETATM 21 C C1B PIO . . . I 7 20.069 -16.005 -12.073 1 217.51 ? C1B PIO 407 A 1 HETATM 22 O O1B PIO . . . I 7 19.355 -15.94 -13.015 1 215.26 ? O1B PIO 407 A 1 HETATM 23 C C1C PIO . . . I 7 24.166 -14.568 -13.803 1 300 ? C1C PIO 407 A 1 HETATM 24 C C2A PIO . . . I 7 24.802 -15.913 -9.372 1 248.73 ? C2A PIO 407 A 1 HETATM 25 C C2B PIO . . . I 7 19.506 -16.131 -10.655 1 205.02 ? C2B PIO 407 A 1 HETATM 26 C C2C PIO . . . I 7 23.366 -14.577 -12.492 1 283.46 ? C2C PIO 407 A 1 HETATM 27 O O2C PIO . . . I 7 23.805 -15.634 -11.682 1 300 ? O2C PIO 407 A 1 HETATM 28 C C3A PIO . . . I 7 24.212 -16.778 -8.264 1 240.89 ? C3A PIO 407 A 1 HETATM 29 C C3B PIO . . . I 7 18.155 -15.422 -10.54 1 195.68 ? C3B PIO 407 A 1 HETATM 30 C C3C PIO . . . I 7 21.886 -14.756 -12.816 1 267.02 ? C3C PIO 407 A 1 HETATM 31 O O3C PIO . . . I 7 21.446 -15.96 -12.26 1 237.19 ? O3C PIO 407 A 1 HETATM 32 O O41 PIO . . . I 7 26.882 -6.894 -17.749 1 300 ? O41 PIO 407 A 1 HETATM 33 O O42 PIO . . . I 7 25.424 -7.876 -16.028 1 300 -1 O42 PIO 407 A 1 HETATM 34 O O43 PIO . . . I 7 24.627 -5.976 -17.396 1 300 ? O43 PIO 407 A 1 HETATM 35 C C4A PIO . . . I 7 23.438 -17.951 -8.86 1 214.13 ? C4A PIO 407 A 1 HETATM 36 C C4B PIO . . . I 7 17.045 -16.366 -10.99 1 182.75 ? C4B PIO 407 A 1 HETATM 37 O O51 PIO . . . I 7 20.604 -8.942 -22.142 1 300 ? O51 PIO 407 A 1 HETATM 38 O O52 PIO . . . I 7 23.052 -9.045 -22.415 1 300 -1 O52 PIO 407 A 1 HETATM 39 O O53 PIO . . . I 7 21.735 -11.127 -22.356 1 300 ? O53 PIO 407 A 1 HETATM 40 C C5A PIO . . . I 7 22.083 -18.03 -8.178 1 201.4 ? C5A PIO 407 A 1 HETATM 41 C C5B PIO . . . I 7 15.838 -16.252 -10.053 1 180.5 ? C5B PIO 407 A 1 HETATM 42 C C6A PIO . . . I 7 21.307 -19.241 -8.674 1 189.72 ? C6A PIO 407 A 1 HETATM 43 C C6B PIO . . . I 7 14.801 -17.3 -10.456 1 178.23 ? C6B PIO 407 A 1 HETATM 44 C C7A PIO . . . I 7 20.508 -19.83 -7.518 1 183.8 ? C7A PIO 407 A 1 HETATM 45 C C7B PIO . . . I 7 13.486 -17.034 -9.719 1 178.57 ? C7B PIO 407 A 1 HETATM 46 C C8A PIO . . . I 7 19.714 -18.726 -6.825 1 180.4 ? C8A PIO 407 A 1 HETATM 47 C C8B PIO . . . I 7 12.417 -18.012 -10.206 1 182.09 ? C8B PIO 407 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 47 #