data_6M84 # _model_server_result.job_id spElGfR3m5rKHlilwZTe4w _model_server_result.datetime_utc '2024-11-15 00:36:29' _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 6m84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":407}' # _entry.id 6M84 # _exptl.entry_id 6M84 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 3 _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 6M84 _cell.length_a 82.787 _cell.length_b 82.787 _cell.length_c 182.976 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id H _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 88 A CYS 123 1_555 A SG CYS 120 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc1 A O THR 108 A THR 143 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.133 ? metalc ? metalc2 A O THR 108 A THR 143 1_555 E K K . A K 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.133 ? metalc ? metalc3 A O THR 108 A THR 143 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? metalc ? metalc4 A OG1 THR 108 A THR 143 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc5 A O THR 108 A THR 143 1_555 F K K . A K 405 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? metalc ? metalc6 A OG1 THR 108 A THR 143 1_555 F K K . A K 405 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc7 A O ILE 109 A ILE 144 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.182 ? metalc ? metalc8 A O ILE 109 A ILE 144 1_555 D K K . A K 403 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.182 ? metalc ? metalc9 A O ILE 109 A ILE 144 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc10 A O ILE 109 A ILE 144 1_555 E K K . A K 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc11 A O GLY 110 A GLY 145 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.208 ? metalc ? metalc12 A O GLY 110 A GLY 145 1_555 C K K . A K 402 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.208 ? metalc ? metalc13 A O GLY 110 A GLY 145 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc14 A O GLY 110 A GLY 145 1_555 D K K . A K 403 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc15 A O TYR 111 A TYR 146 1_555 B K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.391 ? metalc ? metalc16 A O TYR 111 A TYR 146 1_555 B K K . A K 401 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.391 ? metalc ? metalc17 A O TYR 111 A TYR 146 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc18 A O TYR 111 A TYR 146 1_555 C K K . A K 402 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? # _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 342 n n C1 C2 PIO sing 343 n n C1 C6 PIO sing 344 n n C1 H1 PIO sing 345 n n O1 P1 PIO sing 346 n n P1 O11 PIO sing 347 n n O11 H11 PIO sing 348 n n P1 O12 PIO doub 349 n n P1 O13 PIO sing 350 n n C2 O2 PIO sing 351 n n C2 C3 PIO sing 352 n n C2 H2 PIO sing 353 n n O2 HO2 PIO sing 354 n n C3 O3 PIO sing 355 n n C3 C4 PIO sing 356 n n C3 H3 PIO sing 357 n n O3 HO3 PIO sing 358 n n C4 O4 PIO sing 359 n n C4 C5 PIO sing 360 n n C4 H4 PIO sing 361 n n O4 P4 PIO sing 362 n n P4 O41 PIO sing 363 n n O41 H41 PIO sing 364 n n P4 O42 PIO doub 365 n n P4 O43 PIO sing 366 n n O43 H43 PIO sing 367 n n C5 O5 PIO sing 368 n n C5 C6 PIO sing 369 n n C5 H5 PIO sing 370 n n O5 P5 PIO sing 371 n n P5 O51 PIO sing 372 n n O51 H51 PIO sing 373 n n P5 O52 PIO sing 374 n n O52 H52 PIO sing 375 n n P5 O53 PIO doub 376 n n C6 O6 PIO sing 377 n n C6 H6 PIO sing 378 n n O6 HO6 PIO sing 379 n n O13 C1C PIO sing 380 n n C1A O1A PIO doub 381 n n C1A C2A PIO sing 382 n n C1A O2C PIO sing 383 n n C1B O1B PIO doub 384 n n C1B C2B PIO sing 385 n n C1B O3C PIO sing 386 n n C1C C2C PIO sing 387 n n C1C H1C PIO sing 388 n n C1C H1CA PIO sing 389 n n C2A C3A PIO sing 390 n n C2A H2A PIO sing 391 n n C2A H2AA PIO sing 392 n n C2B C3B PIO sing 393 n n C2B H2B PIO sing 394 n n C2B H2BA PIO sing 395 n n C2C O2C PIO sing 396 n n C2C C3C PIO sing 397 n n C2C H2C PIO sing 398 n n C3A C4A PIO sing 399 n n C3A H3A PIO sing 400 n n C3A H3AA PIO sing 401 n n C3B C4B PIO sing 402 n n C3B H3B PIO sing 403 n n C3B H3BA PIO sing 404 n n C3C O3C PIO sing 405 n n C3C H3C PIO sing 406 n n C3C H3CA PIO sing 407 n n C4A C5A PIO sing 408 n n C4A H4A PIO sing 409 n n C4A H4AA PIO sing 410 n n C4B C5B PIO sing 411 n n C4B H4B PIO sing 412 n n C4B H4BA PIO sing 413 n n C5A C6A PIO sing 414 n n C5A H5A PIO sing 415 n n C5A H5AA PIO sing 416 n n C5B C6B PIO sing 417 n n C5B H5B PIO sing 418 n n C5B H5BA PIO sing 419 n n C6A C7A PIO sing 420 n n C6A H6A PIO sing 421 n n C6A H6AA PIO sing 422 n n C6B C7B PIO sing 423 n n C6B H6B PIO sing 424 n n C6B H6BA PIO sing 425 n n C7A C8A PIO sing 426 n n C7A H7A PIO sing 427 n n C7A H7AA PIO sing 428 n n C7B C8B PIO sing 429 n n C7B H7B PIO sing 430 n n C7B H7BA PIO sing 431 n n C8A H8A PIO sing 432 n n C8A H8AA PIO sing 433 n n C8A H8AB PIO sing 434 n n C8B H8B PIO sing 435 n n C8B H8BA PIO sing 436 n n C8B H8BB PIO sing 437 n n # _atom_sites.entry_id 6M84 _atom_sites.fract_transf_matrix[1][1] 0.012079 _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] 0.012079 _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] 0.005465 _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 K A 1 401 370 K K . C 2 K A 1 402 371 K K . D 2 K A 1 403 372 K K . E 2 K A 1 404 373 K K . F 2 K A 1 405 374 K K . G 2 K A 1 406 375 K K . H 3 PIO A 1 407 400 PIO PIO . I 4 LMT A 1 408 601 LMT LMT . J 5 HOH A 1 501 717 HOH HOH . J 5 HOH A 2 502 718 HOH HOH . J 5 HOH A 3 503 713 HOH HOH . J 5 HOH A 4 504 701 HOH HOH . J 5 HOH A 5 505 714 HOH HOH . J 5 HOH A 6 506 702 HOH HOH . J 5 HOH A 7 507 708 HOH HOH . J 5 HOH A 8 508 705 HOH HOH . J 5 HOH A 9 509 703 HOH HOH . J 5 HOH A 10 510 710 HOH HOH . J 5 HOH A 11 511 704 HOH HOH . J 5 HOH A 12 512 709 HOH HOH . J 5 HOH A 13 513 719 HOH HOH . J 5 HOH A 14 514 712 HOH HOH . J 5 HOH A 15 515 716 HOH HOH . J 5 HOH A 16 516 706 HOH HOH . J 5 HOH A 17 517 711 HOH HOH . J 5 HOH A 18 518 707 HOH HOH . J 5 HOH A 19 519 715 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 PIO . . . H 3 10.165 19.736 8.618 1 168.98 ? C1 PIO 407 A 1 HETATM 2 O O1 PIO . . . H 3 10.231 19.524 10.045 1 166.13 ? O1 PIO 407 A 1 HETATM 3 P P1 PIO . . . H 3 9.745 20.518 11.23 1 159.36 ? P1 PIO 407 A 1 HETATM 4 C C2 PIO . . . H 3 10.807 21.044 8.128 1 168.82 ? C2 PIO 407 A 1 HETATM 5 O O2 PIO . . . H 3 10.137 22.194 8.663 1 167.9 ? O2 PIO 407 A 1 HETATM 6 C C3 PIO . . . H 3 10.771 21.107 6.595 1 167.78 ? C3 PIO 407 A 1 HETATM 7 O O3 PIO . . . H 3 11.329 22.347 6.144 1 168.33 ? O3 PIO 407 A 1 HETATM 8 C C4 PIO . . . H 3 9.338 20.951 6.066 1 164.53 ? C4 PIO 407 A 1 HETATM 9 O O4 PIO . . . H 3 9.24 21.062 4.635 1 161.23 ? O4 PIO 407 A 1 HETATM 10 P P4 PIO . . . H 3 10.192 20.364 3.525 1 157.58 ? P4 PIO 407 A 1 HETATM 11 C C5 PIO . . . H 3 8.768 19.623 6.567 1 162.29 ? C5 PIO 407 A 1 HETATM 12 O O5 PIO . . . H 3 7.461 19.367 6.048 1 151.32 ? O5 PIO 407 A 1 HETATM 13 P P5 PIO . . . H 3 7.086 17.913 5.457 1 140.24 ? P5 PIO 407 A 1 HETATM 14 C C6 PIO . . . H 3 8.732 19.648 8.091 1 166.13 ? C6 PIO 407 A 1 HETATM 15 O O6 PIO . . . H 3 8.068 18.48 8.585 1 166.19 ? O6 PIO 407 A 1 HETATM 16 O O11 PIO . . . H 3 9.857 19.752 12.528 1 148.5 ? O11 PIO 407 A 1 HETATM 17 O O12 PIO . . . H 3 8.428 21.169 10.864 1 144.05 ? O12 PIO 407 A 1 HETATM 18 O O13 PIO . . . H 3 10.896 21.654 11.217 1 169.64 ? O13 PIO 407 A 1 HETATM 19 C C1C PIO . . . H 3 12.198 21.448 11.779 1 168.82 ? C1C PIO 407 A 1 HETATM 20 C C2C PIO . . . H 3 13.284 21.847 10.778 1 160.01 ? C2C PIO 407 A 1 HETATM 21 O O41 PIO . . . H 3 11.473 21.165 3.563 1 152.14 ? O41 PIO 407 A 1 HETATM 22 O O42 PIO . . . H 3 9.386 20.536 2.259 1 145.16 ? O42 PIO 407 A 1 HETATM 23 O O43 PIO . . . H 3 10.366 18.923 3.95 1 157.28 ? O43 PIO 407 A 1 HETATM 24 O O51 PIO . . . H 3 7.803 16.924 6.346 1 143.29 ? O51 PIO 407 A 1 HETATM 25 O O52 PIO . . . H 3 5.581 17.836 5.543 1 131.49 ? O52 PIO 407 A 1 HETATM 26 O O53 PIO . . . H 3 7.615 17.92 4.044 1 139.21 ? O53 PIO 407 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #