data_6PW5 # _model_server_result.job_id lTGc1WZQUaD8TehbH6JI1g _model_server_result.datetime_utc '2025-09-01 03:48:43' _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 6pw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 6PW5 # _exptl.entry_id 6PW5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 2 _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 4 _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 6PW5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PW5 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N N 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 668 A CYS 668 1_555 A SG CYS 678 A CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 668 B CYS 668 1_555 B SG CYS 678 B CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 668 C CYS 668 1_555 C SG CYS 678 C CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 D SG CYS 668 D CYS 668 1_555 D SG CYS 678 D CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? # _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 540 n n C1 C2 PIO sing 541 n n C1 C6 PIO sing 542 n n C1 H1 PIO sing 543 n n O1 P1 PIO sing 544 n n P1 O11 PIO sing 545 n n O11 H11 PIO sing 546 n n P1 O12 PIO doub 547 n n P1 O13 PIO sing 548 n n C2 O2 PIO sing 549 n n C2 C3 PIO sing 550 n n C2 H2 PIO sing 551 n n O2 HO2 PIO sing 552 n n C3 O3 PIO sing 553 n n C3 C4 PIO sing 554 n n C3 H3 PIO sing 555 n n O3 HO3 PIO sing 556 n n C4 O4 PIO sing 557 n n C4 C5 PIO sing 558 n n C4 H4 PIO sing 559 n n O4 P4 PIO sing 560 n n P4 O41 PIO sing 561 n n O41 H41 PIO sing 562 n n P4 O42 PIO doub 563 n n P4 O43 PIO sing 564 n n O43 H43 PIO sing 565 n n C5 O5 PIO sing 566 n n C5 C6 PIO sing 567 n n C5 H5 PIO sing 568 n n O5 P5 PIO sing 569 n n P5 O51 PIO sing 570 n n O51 H51 PIO sing 571 n n P5 O52 PIO sing 572 n n O52 H52 PIO sing 573 n n P5 O53 PIO doub 574 n n C6 O6 PIO sing 575 n n C6 H6 PIO sing 576 n n O6 HO6 PIO sing 577 n n O13 C1C PIO sing 578 n n C1A O1A PIO doub 579 n n C1A C2A PIO sing 580 n n C1A O2C PIO sing 581 n n C1B O1B PIO doub 582 n n C1B C2B PIO sing 583 n n C1B O3C PIO sing 584 n n C1C C2C PIO sing 585 n n C1C H1C PIO sing 586 n n C1C H1CA PIO sing 587 n n C2A C3A PIO sing 588 n n C2A H2A PIO sing 589 n n C2A H2AA PIO sing 590 n n C2B C3B PIO sing 591 n n C2B H2B PIO sing 592 n n C2B H2BA PIO sing 593 n n C2C O2C PIO sing 594 n n C2C C3C PIO sing 595 n n C2C H2C PIO sing 596 n n C3A C4A PIO sing 597 n n C3A H3A PIO sing 598 n n C3A H3AA PIO sing 599 n n C3B C4B PIO sing 600 n n C3B H3B PIO sing 601 n n C3B H3BA PIO sing 602 n n C3C O3C PIO sing 603 n n C3C H3C PIO sing 604 n n C3C H3CA PIO sing 605 n n C4A C5A PIO sing 606 n n C4A H4A PIO sing 607 n n C4A H4AA PIO sing 608 n n C4B C5B PIO sing 609 n n C4B H4B PIO sing 610 n n C4B H4BA PIO sing 611 n n C5A C6A PIO sing 612 n n C5A H5A PIO sing 613 n n C5A H5AA PIO sing 614 n n C5B C6B PIO sing 615 n n C5B H5B PIO sing 616 n n C5B H5BA PIO sing 617 n n C6A C7A PIO sing 618 n n C6A H6A PIO sing 619 n n C6A H6AA PIO sing 620 n n C6B C7B PIO sing 621 n n C6B H6B PIO sing 622 n n C6B H6BA PIO sing 623 n n C7A C8A PIO sing 624 n n C7A H7A PIO sing 625 n n C7A H7AA PIO sing 626 n n C7B C8B PIO sing 627 n n C7B H7B PIO sing 628 n n C7B H7BA PIO sing 629 n n C8A H8A PIO sing 630 n n C8A H8AA PIO sing 631 n n C8A H8AB PIO sing 632 n n C8B H8B PIO sing 633 n n C8B H8BA PIO sing 634 n n C8B H8BB PIO sing 635 n n # _atom_sites.entry_id 6PW5 _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 E 2 PIO A 1 1001 1001 PIO PIO . F 3 PCW A 1 1002 1002 PCW PCW . G 4 PIK A 1 1003 1003 PIK PIK . H 2 PIO B 1 1001 1001 PIO PIO . I 3 PCW B 1 1002 1002 PCW PCW . J 4 PIK B 1 1003 1003 PIK PIK . K 2 PIO C 1 1001 1001 PIO PIO . L 3 PCW C 1 1002 1002 PCW PCW . M 4 PIK C 1 1003 1003 PIK PIK . N 2 PIO D 1 1001 1001 PIO PIO . O 3 PCW D 1 1002 1002 PCW PCW . P 4 PIK D 1 1003 1003 PIK PIK . # 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 . . . E 2 82.766 119.307 92.079 1 31.76 ? C1 PIO 1001 A 1 HETATM 2 O O1 PIO . . . E 2 81.755 119.509 91.132 1 31.76 ? O1 PIO 1001 A 1 HETATM 3 P P1 PIO . . . E 2 81.9 120.665 89.97 1 31.76 ? P1 PIO 1001 A 1 HETATM 4 C C2 PIO . . . E 2 82.749 117.811 92.414 1 31.76 ? C2 PIO 1001 A 1 HETATM 5 O O2 PIO . . . E 2 81.755 117.208 91.626 1 31.76 ? O2 PIO 1001 A 1 HETATM 6 C C3 PIO . . . E 2 82.488 117.435 93.885 1 31.76 ? C3 PIO 1001 A 1 HETATM 7 O O3 PIO . . . E 2 81.104 117.3 94.071 1 31.76 ? O3 PIO 1001 A 1 HETATM 8 C C4 PIO . . . E 2 83.021 118.413 94.952 1 31.76 ? C4 PIO 1001 A 1 HETATM 9 O O4 PIO . . . E 2 84.138 117.858 95.602 1 31.76 ? O4 PIO 1001 A 1 HETATM 10 P P4 PIO . . . E 2 84.065 117.559 97.219 1 31.76 ? P4 PIO 1001 A 1 HETATM 11 C C5 PIO . . . E 2 83.43 119.787 94.43 1 31.76 ? C5 PIO 1001 A 1 HETATM 12 O O5 PIO . . . E 2 83.284 120.694 95.486 1 31.76 ? O5 PIO 1001 A 1 HETATM 13 P P5 PIO . . . E 2 84.623 121.374 96.149 1 31.76 ? P5 PIO 1001 A 1 HETATM 14 C C6 PIO . . . E 2 82.522 120.213 93.287 1 31.76 ? C6 PIO 1001 A 1 HETATM 15 O O6 PIO . . . E 2 82.813 121.541 92.975 1 31.76 ? O6 PIO 1001 A 1 HETATM 16 O O11 PIO . . . E 2 81.739 120.015 88.621 1 31.76 ? O11 PIO 1001 A 1 HETATM 17 O O12 PIO . . . E 2 80.817 121.683 90.195 1 31.76 ? O12 PIO 1001 A 1 HETATM 18 O O13 PIO . . . E 2 83.362 121.398 90.068 1 31.76 ? O13 PIO 1001 A 1 HETATM 19 C C1A PIO . . . E 2 83.384 122.381 86.495 1 31.76 ? C1A PIO 1001 A 1 HETATM 20 O O1A PIO . . . E 2 82.681 121.437 86.362 1 31.76 ? O1A PIO 1001 A 1 HETATM 21 C C1B PIO . . . E 2 81.825 126.451 88.752 1 31.76 ? C1B PIO 1001 A 1 HETATM 22 O O1B PIO . . . E 2 82.455 127.229 88.146 1 31.76 ? O1B PIO 1001 A 1 HETATM 23 C C1C PIO . . . E 2 83.44 122.788 90.064 1 31.76 ? C1C PIO 1001 A 1 HETATM 24 C C2A PIO . . . E 2 83.633 123.278 85.287 1 31.76 ? C2A PIO 1001 A 1 HETATM 25 C C2B PIO . . . E 2 80.307 126.572 88.76 1 31.76 ? C2B PIO 1001 A 1 HETATM 26 C C2C PIO . . . E 2 83.194 123.332 88.669 1 31.76 ? C2C PIO 1001 A 1 HETATM 27 O O2C PIO . . . E 2 83.995 122.665 87.73 1 31.76 ? O2C PIO 1001 A 1 HETATM 28 C C3A PIO . . . E 2 82.525 124.316 85.137 1 31.76 ? C3A PIO 1001 A 1 HETATM 29 C C3B PIO . . . E 2 79.864 128.021 88.561 1 31.76 ? C3B PIO 1001 A 1 HETATM 30 C C3C PIO . . . E 2 83.492 124.825 88.716 1 31.76 ? C3C PIO 1001 A 1 HETATM 31 O O3C PIO . . . E 2 82.483 125.439 89.447 1 31.76 ? O3C PIO 1001 A 1 HETATM 32 O O41 PIO . . . E 2 83.219 118.613 97.886 1 31.76 ? O41 PIO 1001 A 1 HETATM 33 O O42 PIO . . . E 2 85.452 117.634 97.807 1 31.76 ? O42 PIO 1001 A 1 HETATM 34 O O43 PIO . . . E 2 83.472 116.193 97.453 1 31.76 ? O43 PIO 1001 A 1 HETATM 35 C C4A PIO . . . E 2 82.809 125.18 83.916 1 31.76 ? C4A PIO 1001 A 1 HETATM 36 C C4B PIO . . . E 2 79.187 128.177 87.205 1 31.76 ? C4B PIO 1001 A 1 HETATM 37 O O51 PIO . . . E 2 85.56 120.312 96.652 1 31.76 ? O51 PIO 1001 A 1 HETATM 38 O O52 PIO . . . E 2 85.327 122.208 95.11 1 31.76 ? O52 PIO 1001 A 1 HETATM 39 O O53 PIO . . . E 2 84.203 122.239 97.312 1 31.76 ? O53 PIO 1001 A 1 HETATM 40 C C5A PIO . . . E 2 84.135 125.905 84.104 1 31.76 ? C5A PIO 1001 A 1 HETATM 41 C C5B PIO . . . E 2 77.868 127.415 87.168 1 31.76 ? C5B PIO 1001 A 1 HETATM 42 C C6A PIO . . . E 2 84.476 126.642 82.817 1 31.76 ? C6A PIO 1001 A 1 HETATM 43 C C6B PIO . . . E 2 77.844 126.442 85.988 1 31.76 ? C6B PIO 1001 A 1 HETATM 44 C C7A PIO . . . E 2 83.503 127.793 82.636 1 31.76 ? C7A PIO 1001 A 1 HETATM 45 C C7B PIO . . . E 2 78.089 127.169 84.673 1 31.76 ? C7B PIO 1001 A 1 HETATM 46 C C8A PIO . . . E 2 83.472 128.159 81.162 1 31.76 ? C8A PIO 1001 A 1 HETATM 47 C C8B PIO . . . E 2 78.715 126.196 83.682 1 31.76 ? C8B PIO 1001 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 393 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 47 #