data_9CC2 # _model_server_result.job_id ju5HTjSNJqA0LW3-LvklzA _model_server_result.datetime_utc '2024-11-25 02:39:52' _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 9cc2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":602}' # _entry.id 9CC2 # _exptl.entry_id 9CC2 _exptl.method 'ELECTRON MICROSCOPY' # _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 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 9CC2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CC2 _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_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 L N N ? 3 N N N ? 3 P 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 E NAG 1 E 1 NAG A 528 NAG 2 n E NAG 2 E 2 NAG A 529 NAG 2 n F NAG 1 F 1 NAG B 528 NAG 2 n F NAG 2 F 2 NAG B 529 NAG 2 n G NAG 1 G 1 NAG C 528 NAG 2 n G NAG 2 G 2 NAG C 529 NAG 2 n H NAG 1 H 1 NAG D 528 NAG 2 n H NAG 2 H 2 NAG D 529 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 disulf ? disulf1 A SG CYS 253 A CYS 253 1_555 A SG CYS 284 A CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 253 B CYS 253 1_555 B SG CYS 284 B CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 C SG CYS 253 C CYS 253 1_555 C SG CYS 284 C CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 D SG CYS 253 D CYS 253 1_555 D SG CYS 284 D CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 230 A ASN 230 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 B ND2 ASN 230 B ASN 230 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C ND2 ASN 230 C ASN 230 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 D ND2 ASN 230 D ASN 230 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 437 n n C1 C2 PIO sing 438 n n C1 C6 PIO sing 439 n n C1 H1 PIO sing 440 n n O1 P1 PIO sing 441 n n P1 O11 PIO sing 442 n n O11 H11 PIO sing 443 n n P1 O12 PIO doub 444 n n P1 O13 PIO sing 445 n n C2 O2 PIO sing 446 n n C2 C3 PIO sing 447 n n C2 H2 PIO sing 448 n n O2 HO2 PIO sing 449 n n C3 O3 PIO sing 450 n n C3 C4 PIO sing 451 n n C3 H3 PIO sing 452 n n O3 HO3 PIO sing 453 n n C4 O4 PIO sing 454 n n C4 C5 PIO sing 455 n n C4 H4 PIO sing 456 n n O4 P4 PIO sing 457 n n P4 O41 PIO sing 458 n n O41 H41 PIO sing 459 n n P4 O42 PIO doub 460 n n P4 O43 PIO sing 461 n n O43 H43 PIO sing 462 n n C5 O5 PIO sing 463 n n C5 C6 PIO sing 464 n n C5 H5 PIO sing 465 n n O5 P5 PIO sing 466 n n P5 O51 PIO sing 467 n n O51 H51 PIO sing 468 n n P5 O52 PIO sing 469 n n O52 H52 PIO sing 470 n n P5 O53 PIO doub 471 n n C6 O6 PIO sing 472 n n C6 H6 PIO sing 473 n n O6 HO6 PIO sing 474 n n O13 C1C PIO sing 475 n n C1A O1A PIO doub 476 n n C1A C2A PIO sing 477 n n C1A O2C PIO sing 478 n n C1B O1B PIO doub 479 n n C1B C2B PIO sing 480 n n C1B O3C PIO sing 481 n n C1C C2C PIO sing 482 n n C1C H1C PIO sing 483 n n C1C H1CA PIO sing 484 n n C2A C3A PIO sing 485 n n C2A H2A PIO sing 486 n n C2A H2AA PIO sing 487 n n C2B C3B PIO sing 488 n n C2B H2B PIO sing 489 n n C2B H2BA PIO sing 490 n n C2C O2C PIO sing 491 n n C2C C3C PIO sing 492 n n C2C H2C PIO sing 493 n n C3A C4A PIO sing 494 n n C3A H3A PIO sing 495 n n C3A H3AA PIO sing 496 n n C3B C4B PIO sing 497 n n C3B H3B PIO sing 498 n n C3B H3BA PIO sing 499 n n C3C O3C PIO sing 500 n n C3C H3C PIO sing 501 n n C3C H3CA PIO sing 502 n n C4A C5A PIO sing 503 n n C4A H4A PIO sing 504 n n C4A H4AA PIO sing 505 n n C4B C5B PIO sing 506 n n C4B H4B PIO sing 507 n n C4B H4BA PIO sing 508 n n C5A C6A PIO sing 509 n n C5A H5A PIO sing 510 n n C5A H5AA PIO sing 511 n n C5B C6B PIO sing 512 n n C5B H5B PIO sing 513 n n C5B H5BA PIO sing 514 n n C6A C7A PIO sing 515 n n C6A H6A PIO sing 516 n n C6A H6AA PIO sing 517 n n C6B C7B PIO sing 518 n n C6B H6B PIO sing 519 n n C6B H6BA PIO sing 520 n n C7A C8A PIO sing 521 n n C7A H7A PIO sing 522 n n C7A H7AA PIO sing 523 n n C7B C8B PIO sing 524 n n C7B H7B PIO sing 525 n n C7B H7BA PIO sing 526 n n C8A H8A PIO sing 527 n n C8A H8AA PIO sing 528 n n C8A H8AB PIO sing 529 n n C8B H8B PIO sing 530 n n C8B H8BA PIO sing 531 n n C8B H8BB PIO sing 532 n n # _atom_sites.entry_id 9CC2 _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 I 3 PIO A 1 601 603 PIO PIO . J 4 FO4 A 1 602 602 FO4 FO4 . K 4 FO4 B 1 601 602 FO4 FO4 . L 3 PIO B 1 602 603 PIO PIO . M 4 FO4 C 1 601 602 FO4 FO4 . N 3 PIO C 1 602 603 PIO PIO . O 4 FO4 D 1 601 602 FO4 FO4 . P 3 PIO D 1 602 603 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 C C1 PIO . . . L 3 128.836 164.893 94.554 1 172.34 ? C1 PIO 602 B 1 HETATM 2 O O1 PIO . . . L 3 128.943 165.606 95.774 1 174.28 ? O1 PIO 602 B 1 HETATM 3 P P1 PIO . . . L 3 130.278 166.463 96.246 1 182.51 ? P1 PIO 602 B 1 HETATM 4 C C2 PIO . . . L 3 129.834 163.722 94.461 1 172.49 ? C2 PIO 602 B 1 HETATM 5 O O2 PIO . . . L 3 131.159 164.195 94.485 1 171.76 ? O2 PIO 602 B 1 HETATM 6 C C3 PIO . . . L 3 129.645 162.947 93.152 1 176.28 ? C3 PIO 602 B 1 HETATM 7 O O3 PIO . . . L 3 130.637 161.955 93.055 1 170.26 ? O3 PIO 602 B 1 HETATM 8 C C4 PIO . . . L 3 129.748 163.881 91.935 1 180.32 ? C4 PIO 602 B 1 HETATM 9 O O4 PIO . . . L 3 129.562 163.18 90.723 1 181.66 ? O4 PIO 602 B 1 HETATM 10 P P4 PIO . . . L 3 128.452 161.969 90.558 1 184.28 ? P4 PIO 602 B 1 HETATM 11 C C5 PIO . . . L 3 128.753 165.051 92.029 1 178.47 ? C5 PIO 602 B 1 HETATM 12 O O5 PIO . . . L 3 128.883 165.928 90.929 1 181.68 ? O5 PIO 602 B 1 HETATM 13 P P5 PIO . . . L 3 130.356 166.38 90.334 1 191.09 ? P5 PIO 602 B 1 HETATM 14 C C6 PIO . . . L 3 128.923 165.833 93.338 1 173.39 ? C6 PIO 602 B 1 HETATM 15 O O6 PIO . . . L 3 127.911 166.806 93.427 1 166.84 ? O6 PIO 602 B 1 HETATM 16 O O11 PIO . . . L 3 129.876 167.892 96.52 1 170.09 ? O11 PIO 602 B 1 HETATM 17 O O12 PIO . . . L 3 131.359 166.442 95.191 1 176.69 ? O12 PIO 602 B 1 HETATM 18 O O13 PIO . . . L 3 130.871 165.793 97.631 1 173.85 ? O13 PIO 602 B 1 HETATM 19 C C1A PIO . . . L 3 134.255 165.205 96.279 1 170.07 ? C1A PIO 602 B 1 HETATM 20 O O1A PIO . . . L 3 134.256 166.26 95.737 1 173.28 ? O1A PIO 602 B 1 HETATM 21 C C1B PIO . . . L 3 134.36 162.909 100.52 1 141.39 ? C1B PIO 602 B 1 HETATM 22 O O1B PIO . . . L 3 133.51 162.085 100.554 1 129.99 ? O1B PIO 602 B 1 HETATM 23 C C1C PIO . . . L 3 131.895 166.455 98.319 1 168.1 ? C1C PIO 602 B 1 HETATM 24 C C2A PIO . . . L 3 135.407 164.228 96.056 1 161.5 ? C2A PIO 602 B 1 HETATM 25 C C2B PIO . . . L 3 135.5 162.871 101.534 1 133.79 ? C2B PIO 602 B 1 HETATM 26 C C2C PIO . . . L 3 133.151 165.587 98.313 1 167.55 ? C2C PIO 602 B 1 HETATM 27 O O2C PIO . . . L 3 133.198 164.852 97.123 1 171.71 ? O2C PIO 602 B 1 HETATM 28 C C3A PIO . . . L 3 136.682 164.988 95.694 1 155.94 ? C3A PIO 602 B 1 HETATM 29 C C3B PIO . . . L 3 135.114 161.975 102.707 1 118.64 ? C3B PIO 602 B 1 HETATM 30 C C3C PIO . . . L 3 133.119 164.625 99.5 1 159.02 ? C3C PIO 602 B 1 HETATM 31 O O3C PIO . . . L 3 134.321 163.913 99.546 1 156.5 ? O3C PIO 602 B 1 HETATM 32 O O41 PIO . . . L 3 128.134 161.804 89.092 1 174.11 ? O41 PIO 602 B 1 HETATM 33 O O42 PIO . . . L 3 129.021 160.668 91.075 1 172.52 ? O42 PIO 602 B 1 HETATM 34 O O43 PIO . . . L 3 127.178 162.302 91.297 1 173.61 ? O43 PIO 602 B 1 HETATM 35 C C4A PIO . . . L 3 137.245 165.704 96.922 1 153.6 ? C4A PIO 602 B 1 HETATM 36 C C4B PIO . . . L 3 135.833 160.634 102.586 1 116.44 ? C4B PIO 602 B 1 HETATM 37 O O51 PIO . . . L 3 130.834 165.357 89.33 1 185.64 ? O51 PIO 602 B 1 HETATM 38 O O52 PIO . . . L 3 131.375 166.522 91.44 1 182.61 ? O52 PIO 602 B 1 HETATM 39 O O53 PIO . . . L 3 130.21 167.712 89.637 1 179.84 ? O53 PIO 602 B 1 HETATM 40 C C5A PIO . . . L 3 137.196 164.784 98.141 1 157.2 ? C5A PIO 602 B 1 HETATM 41 C C5B PIO . . . L 3 137.342 160.854 102.666 1 124.4 ? C5B PIO 602 B 1 HETATM 42 C C6A PIO . . . L 3 138.53 164.827 98.883 1 148.88 ? C6A PIO 602 B 1 HETATM 43 C C6B PIO . . . L 3 138.06 159.527 102.438 1 118.98 ? C6B PIO 602 B 1 HETATM 44 C C7A PIO . . . L 3 138.692 163.548 99.7 1 145.1 ? C7A PIO 602 B 1 HETATM 45 C C7B PIO . . . L 3 139.568 159.759 102.394 1 124.44 ? C7B PIO 602 B 1 HETATM 46 C C8A PIO . . . L 3 139.774 163.747 100.759 1 133.93 ? C8A PIO 602 B 1 HETATM 47 C C8B PIO . . . L 3 140.108 159.869 103.817 1 117.3 ? C8B PIO 602 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 47 #