data_6VM0 # _model_server_result.job_id '_O0zhefoW8zkuwdpogpBFg' _model_server_result.datetime_utc '2024-11-28 09:30:56' _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 6vm0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":902}' # _entry.id 6VM0 # _exptl.entry_id 6VM0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 3 _entity.src_method man _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 5 _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 6VM0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VM0 _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_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 _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 ? _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 ? 3 K N N ? 3 O N N ? 3 Q N N ? 3 V N N ? 3 Y 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 902 NAG 2 n F NAG 2 F 2 NAG A 903 NAG 2 n G NAG 1 G 1 NAG E 902 NAG 2 n G NAG 2 G 2 NAG E 903 NAG 2 n H NAG 1 H 1 NAG C 902 NAG 2 n H NAG 2 H 2 NAG C 903 NAG 2 n I NAG 1 I 1 NAG B 902 NAG 2 n I NAG 2 I 2 NAG B 903 NAG 2 n J NAG 1 J 1 NAG D 902 NAG 2 n J NAG 2 J 2 NAG D 903 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 covale ? covale1 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 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 430 n n C1 C2 PIO sing 431 n n C1 C6 PIO sing 432 n n C1 H1 PIO sing 433 n n O1 P1 PIO sing 434 n n P1 O11 PIO sing 435 n n O11 H11 PIO sing 436 n n P1 O12 PIO doub 437 n n P1 O13 PIO sing 438 n n C2 O2 PIO sing 439 n n C2 C3 PIO sing 440 n n C2 H2 PIO sing 441 n n O2 HO2 PIO sing 442 n n C3 O3 PIO sing 443 n n C3 C4 PIO sing 444 n n C3 H3 PIO sing 445 n n O3 HO3 PIO sing 446 n n C4 O4 PIO sing 447 n n C4 C5 PIO sing 448 n n C4 H4 PIO sing 449 n n O4 P4 PIO sing 450 n n P4 O41 PIO sing 451 n n O41 H41 PIO sing 452 n n P4 O42 PIO doub 453 n n P4 O43 PIO sing 454 n n O43 H43 PIO sing 455 n n C5 O5 PIO sing 456 n n C5 C6 PIO sing 457 n n C5 H5 PIO sing 458 n n O5 P5 PIO sing 459 n n P5 O51 PIO sing 460 n n O51 H51 PIO sing 461 n n P5 O52 PIO sing 462 n n O52 H52 PIO sing 463 n n P5 O53 PIO doub 464 n n C6 O6 PIO sing 465 n n C6 H6 PIO sing 466 n n O6 HO6 PIO sing 467 n n O13 C1C PIO sing 468 n n C1A O1A PIO doub 469 n n C1A C2A PIO sing 470 n n C1A O2C PIO sing 471 n n C1B O1B PIO doub 472 n n C1B C2B PIO sing 473 n n C1B O3C PIO sing 474 n n C1C C2C PIO sing 475 n n C1C H1C PIO sing 476 n n C1C H1CA PIO sing 477 n n C2A C3A PIO sing 478 n n C2A H2A PIO sing 479 n n C2A H2AA PIO sing 480 n n C2B C3B PIO sing 481 n n C2B H2B PIO sing 482 n n C2B H2BA PIO sing 483 n n C2C O2C PIO sing 484 n n C2C C3C PIO sing 485 n n C2C H2C PIO sing 486 n n C3A C4A PIO sing 487 n n C3A H3A PIO sing 488 n n C3A H3AA PIO sing 489 n n C3B C4B PIO sing 490 n n C3B H3B PIO sing 491 n n C3B H3BA PIO sing 492 n n C3C O3C PIO sing 493 n n C3C H3C PIO sing 494 n n C3C H3CA PIO sing 495 n n C4A C5A PIO sing 496 n n C4A H4A PIO sing 497 n n C4A H4AA PIO sing 498 n n C4B C5B PIO sing 499 n n C4B H4B PIO sing 500 n n C4B H4BA PIO sing 501 n n C5A C6A PIO sing 502 n n C5A H5A PIO sing 503 n n C5A H5AA PIO sing 504 n n C5B C6B PIO sing 505 n n C5B H5B PIO sing 506 n n C5B H5BA PIO sing 507 n n C6A C7A PIO sing 508 n n C6A H6A PIO sing 509 n n C6A H6AA PIO sing 510 n n C6B C7B PIO sing 511 n n C6B H6B PIO sing 512 n n C6B H6BA PIO sing 513 n n C7A C8A PIO sing 514 n n C7A H7A PIO sing 515 n n C7A H7AA PIO sing 516 n n C7B C8B PIO sing 517 n n C7B H7B PIO sing 518 n n C7B H7BA PIO sing 519 n n C8A H8A PIO sing 520 n n C8A H8AA PIO sing 521 n n C8A H8AB PIO sing 522 n n C8B H8B PIO sing 523 n n C8B H8BA PIO sing 524 n n C8B H8BB PIO sing 525 n n # _atom_sites.entry_id 6VM0 _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 PIO A 1 801 801 PIO PIO . L 4 GLY A 1 804 601 GLY GLY . M 5 IVM A 1 805 901 IVM IVM . N 5 IVM E 1 901 901 IVM IVM . O 3 PIO E 1 902 801 PIO PIO . P 4 GLY E 1 905 601 GLY GLY . Q 3 PIO C 1 801 801 PIO PIO . R 4 GLY C 1 804 601 GLY GLY . S 5 IVM C 1 805 901 IVM IVM . T 4 GLY B 1 601 601 GLY GLY . U 5 IVM B 1 602 901 IVM IVM . V 3 PIO B 1 603 801 PIO PIO . W 5 IVM D 1 901 901 IVM IVM . X 4 GLY D 1 902 601 GLY GLY . Y 3 PIO D 1 903 801 PIO PIO . # 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 O O1 PIO . . . O 3 152.947 130.453 123.338 1 111.39 ? O1 PIO 902 E 1 HETATM 2 P P1 PIO . . . O 3 151.632 131.305 123.849 1 111.39 ? P1 PIO 902 E 1 HETATM 3 O O11 PIO . . . O 3 150.837 131.729 122.64 1 111.39 ? O11 PIO 902 E 1 HETATM 4 O O12 PIO . . . O 3 150.791 130.461 124.773 1 111.39 ? O12 PIO 902 E 1 HETATM 5 O O13 PIO . . . O 3 152.158 132.629 124.659 1 111.39 ? O13 PIO 902 E 1 HETATM 6 C C1A PIO . . . O 3 155.712 133.875 127.008 1 111.39 ? C1A PIO 902 E 1 HETATM 7 O O1A PIO . . . O 3 156.277 133.652 125.989 1 111.39 ? O1A PIO 902 E 1 HETATM 8 C C1B PIO . . . O 3 151.477 133.006 129.527 1 111.39 ? C1B PIO 902 E 1 HETATM 9 O O1B PIO . . . O 3 151.173 131.868 129.425 1 111.39 ? O1B PIO 902 E 1 HETATM 10 C C1C PIO . . . O 3 153.331 132.462 125.388 1 111.39 ? C1C PIO 902 E 1 HETATM 11 C C2A PIO . . . O 3 156.33 134.883 127.96 1 111.39 ? C2A PIO 902 E 1 HETATM 12 C C2B PIO . . . O 3 150.863 133.864 130.618 1 111.39 ? C2B PIO 902 E 1 HETATM 13 C C2C PIO . . . O 3 153.412 133.498 126.505 1 111.39 ? C2C PIO 902 E 1 HETATM 14 O O2C PIO . . . O 3 154.51 133.224 127.334 1 111.39 ? O2C PIO 902 E 1 HETATM 15 C C3A PIO . . . O 3 155.49 135.005 129.225 1 111.39 ? C3A PIO 902 E 1 HETATM 16 C C3B PIO . . . O 3 150.594 133.007 131.844 1 111.39 ? C3B PIO 902 E 1 HETATM 17 C C3C PIO . . . O 3 152.109 133.465 127.302 1 111.39 ? C3C PIO 902 E 1 HETATM 18 O O3C PIO . . . O 3 152.407 133.584 128.659 1 111.39 ? O3C PIO 902 E 1 HETATM 19 C C4A PIO . . . O 3 156.396 135.454 130.366 1 111.39 ? C4A PIO 902 E 1 HETATM 20 C C4B PIO . . . O 3 151.797 133.1 132.77 1 111.39 ? C4B PIO 902 E 1 HETATM 21 C C5A PIO . . . O 3 156.816 134.254 131.215 1 111.39 ? C5A PIO 902 E 1 HETATM 22 C C5B PIO . . . O 3 151.629 134.327 133.661 1 111.39 ? C5B PIO 902 E 1 HETATM 23 C C6A PIO . . . O 3 157.38 134.775 132.536 1 111.39 ? C6A PIO 902 E 1 HETATM 24 C C6B PIO . . . O 3 151.124 133.876 135.029 1 111.39 ? C6B PIO 902 E 1 HETATM 25 C C7A PIO . . . O 3 157.51 133.634 133.545 1 111.39 ? C7A PIO 902 E 1 HETATM 26 C C7B PIO . . . O 3 152.279 133.301 135.844 1 111.39 ? C7B PIO 902 E 1 HETATM 27 C C8A PIO . . . O 3 157.942 134.19 134.899 1 111.39 ? C8A PIO 902 E 1 HETATM 28 C C8B PIO . . . O 3 151.746 132.882 137.215 1 111.39 ? C8B PIO 902 E 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #