data_8YR2 # _model_server_result.job_id RQdr2t8OL4DheBpXMeKmJg _model_server_result.datetime_utc '2025-03-03 20:28:32' _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 8yr2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"FA","auth_seq_id":712}' # _entry.id 8YR2 # _exptl.entry_id 8YR2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 586.607 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-2-octanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,4,5,6-pentakis(oxidanyl)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 8YR2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YR2 _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 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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA _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 ? 7 O N N ? 7 P N N ? 7 EA N N ? 7 FA 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 metalc ? metalc1 A O GLY 71 B GLY 71 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc2 A O ALA 73 B ALA 73 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc3 A O VAL 74 B VAL 74 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc4 A OD1 ASN 78 B ASN 78 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc5 A O SER 318 B SER 318 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc6 A OD1 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc7 A OD2 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.177 ? metalc ? metalc8 A OG SER 419 B SER 419 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc9 B O GLY 71 A GLY 71 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc10 B O VAL 74 A VAL 74 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc11 B OD1 ASN 78 A ASN 78 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc12 B O SER 318 A SER 318 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc13 B O LEU 415 A LEU 415 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc14 B OD2 ASP 418 A ASP 418 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc15 B OG SER 419 A SER 419 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? # _chem_comp.formula 'C25 H47 O13 P' _chem_comp.formula_weight 586.607 _chem_comp.id A1LX7 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-2-octanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C02 C01 A1LX7 sing 43 n n C02 C03 A1LX7 sing 44 n n C03 C04 A1LX7 sing 45 n n C04 C05 A1LX7 sing 46 n n C05 C06 A1LX7 sing 47 n n C19 C20 A1LX7 sing 48 n n C19 C18 A1LX7 sing 49 n n C06 C07 A1LX7 sing 50 n n C07 C08 A1LX7 sing 51 n n C18 C17 A1LX7 sing 52 n n O39 C08 A1LX7 doub 53 n n C08 O09 A1LX7 sing 54 n n C17 C16 A1LX7 sing 55 n n O09 C10 A1LX7 sing 56 n n C16 C15 A1LX7 sing 57 n n C10 C11 A1LX7 sing 58 n n C15 C14 A1LX7 sing 59 n n C14 C13 A1LX7 sing 60 n n C11 O12 A1LX7 sing 61 n n C11 C22 A1LX7 sing 62 n n O12 C13 A1LX7 sing 63 n n C13 O21 A1LX7 doub 64 n n C22 O23 A1LX7 sing 65 n n O23 P24 A1LX7 sing 66 n n O38 P24 A1LX7 doub 67 n n P24 O26 A1LX7 sing 68 n n P24 O25 A1LX7 sing 69 n n O26 C27 A1LX7 sing 70 n n O37 C36 A1LX7 sing 71 n n C27 C36 A1LX7 sing 72 n n C27 C28 A1LX7 sing 73 n n C36 C34 A1LX7 sing 74 n n O29 C28 A1LX7 sing 75 n n C28 C30 A1LX7 sing 76 n n C34 O35 A1LX7 sing 77 n n C34 C32 A1LX7 sing 78 n n C30 C32 A1LX7 sing 79 n n C30 O31 A1LX7 sing 80 n n C32 O33 A1LX7 sing 81 n n C10 H1 A1LX7 sing 82 n n C10 H2 A1LX7 sing 83 n n C15 H3 A1LX7 sing 84 n n C15 H4 A1LX7 sing 85 n n C16 H5 A1LX7 sing 86 n n C16 H6 A1LX7 sing 87 n n C17 H7 A1LX7 sing 88 n n C17 H8 A1LX7 sing 89 n n C18 H9 A1LX7 sing 90 n n C18 H10 A1LX7 sing 91 n n C19 H11 A1LX7 sing 92 n n C19 H12 A1LX7 sing 93 n n C20 H13 A1LX7 sing 94 n n C20 H14 A1LX7 sing 95 n n C20 H15 A1LX7 sing 96 n n C28 H16 A1LX7 sing 97 n n C32 H17 A1LX7 sing 98 n n C22 H18 A1LX7 sing 99 n n C22 H19 A1LX7 sing 100 n n C11 H20 A1LX7 sing 101 n n C01 H21 A1LX7 sing 102 n n C01 H22 A1LX7 sing 103 n n C01 H23 A1LX7 sing 104 n n C02 H24 A1LX7 sing 105 n n C02 H25 A1LX7 sing 106 n n C03 H26 A1LX7 sing 107 n n C03 H27 A1LX7 sing 108 n n C04 H28 A1LX7 sing 109 n n C04 H29 A1LX7 sing 110 n n C05 H30 A1LX7 sing 111 n n C05 H31 A1LX7 sing 112 n n C06 H32 A1LX7 sing 113 n n C06 H33 A1LX7 sing 114 n n C07 H34 A1LX7 sing 115 n n C07 H35 A1LX7 sing 116 n n C14 H36 A1LX7 sing 117 n n C14 H37 A1LX7 sing 118 n n O25 H38 A1LX7 sing 119 n n C27 H39 A1LX7 sing 120 n n O29 H40 A1LX7 sing 121 n n C30 H41 A1LX7 sing 122 n n O31 H42 A1LX7 sing 123 n n O33 H43 A1LX7 sing 124 n n C34 H44 A1LX7 sing 125 n n O35 H45 A1LX7 sing 126 n n C36 H46 A1LX7 sing 127 n n O37 H47 A1LX7 sing 128 n n # _atom_sites.entry_id 8YR2 _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 C 2 41U B 1 701 701 41U 41U . D 3 PIO B 1 702 702 PIO PIO . E 4 NA B 1 703 12 NA NA . F 4 NA B 1 704 13 NA NA . G 5 CL B 1 705 6 CL CL . H 6 CLR B 1 706 704 CLR CLR . I 6 CLR B 1 707 706 CLR CLR . J 6 CLR B 1 708 709 CLR CLR . K 6 CLR B 1 709 710 CLR CLR . L 6 CLR B 1 710 712 CLR CLR . M 6 CLR B 1 711 713 CLR CLR . N 6 CLR B 1 712 714 CLR CLR . O 7 A1LX7 B 1 713 705 A1LX7 PI0 . P 7 A1LX7 B 1 714 716 A1LX7 PI0 . Q 6 CLR B 1 715 701 CLR CLR . R 6 CLR B 1 716 702 CLR CLR . S 6 CLR B 1 717 703 CLR CLR . T 6 CLR B 1 718 704 CLR CLR . U 2 41U A 1 701 701 41U 41U . V 3 PIO A 1 702 702 PIO PIO . W 4 NA A 1 703 10 NA NA . X 4 NA A 1 704 11 NA NA . Y 5 CL A 1 705 5 CL CL . Z 6 CLR A 1 706 707 CLR CLR . AA 6 CLR A 1 707 708 CLR CLR . BA 6 CLR A 1 708 711 CLR CLR . CA 6 CLR A 1 709 715 CLR CLR . DA 6 CLR A 1 710 718 CLR CLR . EA 7 A1LX7 A 1 711 712 A1LX7 PI0 . FA 7 A1LX7 A 1 712 713 A1LX7 PI0 . GA 6 CLR A 1 713 707 CLR CLR . HA 6 CLR A 1 714 708 CLR CLR . IA 6 CLR A 1 715 709 CLR CLR . JA 6 CLR A 1 716 713 CLR CLR . KA 8 HOH B 1 801 7 HOH HOH . KA 8 HOH B 2 802 6 HOH HOH . KA 8 HOH B 3 803 5 HOH HOH . LA 8 HOH A 1 801 4 HOH HOH . LA 8 HOH A 2 802 3 HOH HOH . LA 8 HOH A 3 803 1 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 C10 A1LX7 . . . FA 7 73.391 98.03 83.893 1 30 ? C10 A1LX7 712 A 1 HETATM 2 C C15 A1LX7 . . . FA 7 77.235 98.062 84.524 1 30 ? C15 A1LX7 712 A 1 HETATM 3 C C16 A1LX7 . . . FA 7 78.572 97.808 85.206 1 30 ? C16 A1LX7 712 A 1 HETATM 4 C C17 A1LX7 . . . FA 7 78.652 98.409 86.602 1 30 ? C17 A1LX7 712 A 1 HETATM 5 C C18 A1LX7 . . . FA 7 78.829 97.35 87.684 1 30 ? C18 A1LX7 712 A 1 HETATM 6 C C19 A1LX7 . . . FA 7 80.283 96.923 87.844 1 30 ? C19 A1LX7 712 A 1 HETATM 7 C C20 A1LX7 . . . FA 7 80.789 97.101 89.272 1 30 ? C20 A1LX7 712 A 1 HETATM 8 C C28 A1LX7 . . . FA 7 74.717 98.495 78.459 1 30 ? C28 A1LX7 712 A 1 HETATM 9 C C32 A1LX7 . . . FA 7 75.396 99.048 76.015 1 30 ? C32 A1LX7 712 A 1 HETATM 10 C C22 A1LX7 . . . FA 7 72.662 97.621 81.577 1 30 ? C22 A1LX7 712 A 1 HETATM 11 C C11 A1LX7 . . . FA 7 73.743 98.264 82.43 1 30 ? C11 A1LX7 712 A 1 HETATM 12 C C13 A1LX7 . . . FA 7 76.127 98.28 82.236 1 30 ? C13 A1LX7 712 A 1 HETATM 13 C C01 A1LX7 . . . FA 7 75.987 97.584 90.907 1 30 ? C01 A1LX7 712 A 1 HETATM 14 C C02 A1LX7 . . . FA 7 74.777 97.8 90.001 1 30 ? C02 A1LX7 712 A 1 HETATM 15 C C03 A1LX7 . . . FA 7 75.168 98.324 88.623 1 30 ? C03 A1LX7 712 A 1 HETATM 16 C C04 A1LX7 . . . FA 7 74.193 97.864 87.548 1 30 ? C04 A1LX7 712 A 1 HETATM 17 C C05 A1LX7 . . . FA 7 72.81 97.614 88.134 1 30 ? C05 A1LX7 712 A 1 HETATM 18 C C06 A1LX7 . . . FA 7 71.865 96.943 87.144 1 30 ? C06 A1LX7 712 A 1 HETATM 19 C C07 A1LX7 . . . FA 7 71.045 97.967 86.372 1 30 ? C07 A1LX7 712 A 1 HETATM 20 C C08 A1LX7 . . . FA 7 71.242 97.896 84.863 1 30 ? C08 A1LX7 712 A 1 HETATM 21 O O09 A1LX7 . . . FA 7 72.209 98.691 84.239 1 30 ? O09 A1LX7 712 A 1 HETATM 22 O O12 A1LX7 . . . FA 7 74.926 97.583 82.142 1 30 ? O12 A1LX7 712 A 1 HETATM 23 C C14 A1LX7 . . . FA 7 77.29 97.714 83.042 1 30 ? C14 A1LX7 712 A 1 HETATM 24 O O21 A1LX7 . . . FA 7 76.25 99.296 81.665 1 30 ? O21 A1LX7 712 A 1 HETATM 25 O O23 A1LX7 . . . FA 7 71.649 98.534 81.298 1 30 ? O23 A1LX7 712 A 1 HETATM 26 P P24 A1LX7 . . . FA 7 71.239 98.799 79.731 1 30 ? P24 A1LX7 712 A 1 HETATM 27 O O25 A1LX7 . . . FA 7 70.672 97.549 79.116 1 30 ? O25 A1LX7 712 A 1 HETATM 28 O O26 A1LX7 . . . FA 7 72.549 99.348 78.893 1 30 ? O26 A1LX7 712 A 1 HETATM 29 C C27 A1LX7 . . . FA 7 73.242 98.517 78.004 1 30 ? C27 A1LX7 712 A 1 HETATM 30 O O29 A1LX7 . . . FA 7 74.941 99.591 79.295 1 30 ? O29 A1LX7 712 A 1 HETATM 31 C C30 A1LX7 . . . FA 7 75.818 98.519 77.387 1 30 ? C30 A1LX7 712 A 1 HETATM 32 O O31 A1LX7 . . . FA 7 76.848 99.322 77.89 1 30 ? O31 A1LX7 712 A 1 HETATM 33 O O33 A1LX7 . . . FA 7 76.347 98.656 75.059 1 30 ? O33 A1LX7 712 A 1 HETATM 34 C C34 A1LX7 . . . FA 7 74.046 98.459 75.629 1 30 ? C34 A1LX7 712 A 1 HETATM 35 O O35 A1LX7 . . . FA 7 73.731 98.804 74.309 1 30 ? O35 A1LX7 712 A 1 HETATM 36 C C36 A1LX7 . . . FA 7 72.99 99.01 76.579 1 30 ? C36 A1LX7 712 A 1 HETATM 37 O O37 A1LX7 . . . FA 7 71.732 98.554 76.158 1 30 ? O37 A1LX7 712 A 1 HETATM 38 O O38 A1LX7 . . . FA 7 70.173 99.863 79.704 1 30 ? O38 A1LX7 712 A 1 HETATM 39 O O39 A1LX7 . . . FA 7 70.558 97.179 84.219 1 30 ? O39 A1LX7 712 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #