data_8DDU # _model_server_result.job_id jB2YcgKnPGrsMcuEp7g__Q _model_server_result.datetime_utc '2024-11-22 13:08:45' _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 8ddu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1401}' # _entry.id 8DDU # _exptl.entry_id 8DDU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 704.998 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _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 8DDU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DDU _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _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 I N N ? 3 N N N ? 3 Q N N ? 3 T N N # _chem_comp.formula 'C39 H77 O8 P' _chem_comp.formula_weight 704.998 _chem_comp.id 3PH _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDIC ACID' # 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 O13 P 3PH sing 1 n n O13 H13 3PH sing 2 n n P O14 3PH sing 3 n n P O12 3PH doub 4 n n P O11 3PH sing 5 n n O11 C1 3PH sing 6 n n C1 C2 3PH sing 7 n n C1 H11 3PH sing 8 n n C1 H12 3PH sing 9 n n C2 O21 3PH sing 10 n n C2 C3 3PH sing 11 n n C2 H2 3PH sing 12 n n O21 C21 3PH sing 13 n n C21 O22 3PH doub 14 n n C21 C22 3PH sing 15 n n C22 C23 3PH sing 16 n n C22 H221 3PH sing 17 n n C22 H222 3PH sing 18 n n C23 C24 3PH sing 19 n n C23 H231 3PH sing 20 n n C23 H232 3PH sing 21 n n C24 C25 3PH sing 22 n n C24 H241 3PH sing 23 n n C24 H242 3PH sing 24 n n C25 C26 3PH sing 25 n n C25 H251 3PH sing 26 n n C25 H252 3PH sing 27 n n C26 C27 3PH sing 28 n n C26 H261 3PH sing 29 n n C26 H262 3PH sing 30 n n C27 C28 3PH sing 31 n n C27 H271 3PH sing 32 n n C27 H272 3PH sing 33 n n C28 C29 3PH sing 34 n n C28 H281 3PH sing 35 n n C28 H282 3PH sing 36 n n C29 C2A 3PH sing 37 n n C29 H291 3PH sing 38 n n C29 H292 3PH sing 39 n n C2A C2B 3PH sing 40 n n C2A H2A1 3PH sing 41 n n C2A H2A2 3PH sing 42 n n C2B C2C 3PH sing 43 n n C2B H2B1 3PH sing 44 n n C2B H2B2 3PH sing 45 n n C2C C2D 3PH sing 46 n n C2C H2C1 3PH sing 47 n n C2C H2C2 3PH sing 48 n n C2D C2E 3PH sing 49 n n C2D H2D1 3PH sing 50 n n C2D H2D2 3PH sing 51 n n C2E C2F 3PH sing 52 n n C2E H2E1 3PH sing 53 n n C2E H2E2 3PH sing 54 n n C2F C2G 3PH sing 55 n n C2F H2F1 3PH sing 56 n n C2F H2F2 3PH sing 57 n n C2G C2H 3PH sing 58 n n C2G H2G1 3PH sing 59 n n C2G H2G2 3PH sing 60 n n C2H C2I 3PH sing 61 n n C2H H2H1 3PH sing 62 n n C2H H2H2 3PH sing 63 n n C2I H2I1 3PH sing 64 n n C2I H2I2 3PH sing 65 n n C2I H2I3 3PH sing 66 n n C3 O31 3PH sing 67 n n C3 H31 3PH sing 68 n n C3 H32 3PH sing 69 n n O31 C31 3PH sing 70 n n C31 O32 3PH doub 71 n n C31 C32 3PH sing 72 n n C32 C33 3PH sing 73 n n C32 H321 3PH sing 74 n n C32 H322 3PH sing 75 n n C33 C34 3PH sing 76 n n C33 H331 3PH sing 77 n n C33 H332 3PH sing 78 n n C34 C35 3PH sing 79 n n C34 H341 3PH sing 80 n n C34 H342 3PH sing 81 n n C35 C36 3PH sing 82 n n C35 H351 3PH sing 83 n n C35 H352 3PH sing 84 n n C36 C37 3PH sing 85 n n C36 H361 3PH sing 86 n n C36 H362 3PH sing 87 n n C37 C38 3PH sing 88 n n C37 H371 3PH sing 89 n n C37 H372 3PH sing 90 n n C38 C39 3PH sing 91 n n C38 H381 3PH sing 92 n n C38 H382 3PH sing 93 n n C39 C3A 3PH sing 94 n n C39 H391 3PH sing 95 n n C39 H392 3PH sing 96 n n C3A C3B 3PH sing 97 n n C3A H3A1 3PH sing 98 n n C3A H3A2 3PH sing 99 n n C3B C3C 3PH sing 100 n n C3B H3B1 3PH sing 101 n n C3B H3B2 3PH sing 102 n n C3C C3D 3PH sing 103 n n C3C H3C1 3PH sing 104 n n C3C H3C2 3PH sing 105 n n C3D C3E 3PH sing 106 n n C3D H3D1 3PH sing 107 n n C3D H3D2 3PH sing 108 n n C3E C3F 3PH sing 109 n n C3E H3E1 3PH sing 110 n n C3E H3E2 3PH sing 111 n n C3F C3G 3PH sing 112 n n C3F H3F1 3PH sing 113 n n C3F H3F2 3PH sing 114 n n C3G C3H 3PH sing 115 n n C3G H3G1 3PH sing 116 n n C3G H3G2 3PH sing 117 n n C3H C3I 3PH sing 118 n n C3H H3H1 3PH sing 119 n n C3H H3H2 3PH sing 120 n n C3I H3I1 3PH sing 121 n n C3I H3I2 3PH sing 122 n n C3I H3I3 3PH sing 123 n n O14 H77 3PH sing 124 n n # _atom_sites.entry_id 8DDU _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 3PH A 1 1401 1401 3PH 3PH . J 4 9Z9 A 1 1402 1402 9Z9 9Z9 . K 5 PIO A 1 1403 1403 PIO PIO . L 6 NA A 1 1404 1 NA NA . M 6 NA A 1 1405 2 NA NA . N 3 3PH B 1 1401 1401 3PH 3PH . O 4 9Z9 B 1 1402 1402 9Z9 9Z9 . P 5 PIO B 1 1403 1403 PIO PIO . Q 3 3PH C 1 1401 1401 3PH 3PH . R 4 9Z9 C 1 1402 1402 9Z9 9Z9 . S 5 PIO C 1 1403 1403 PIO PIO . T 3 3PH D 1 1401 1401 3PH 3PH . U 4 9Z9 D 1 1402 1402 9Z9 9Z9 . V 5 PIO D 1 1403 1403 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 O13 3PH . . . I 3 234.84 203.06 220.048 1 32.33 ? O13 3PH 1401 A 1 HETATM 2 P P 3PH . . . I 3 235.911 203.645 220.945 1 32.33 ? P 3PH 1401 A 1 HETATM 3 O O14 3PH . . . I 3 236.953 202.592 221.245 1 32.33 ? O14 3PH 1401 A 1 HETATM 4 O O12 3PH . . . I 3 236.56 204.825 220.257 1 32.33 ? O12 3PH 1401 A 1 HETATM 5 O O11 3PH . . . I 3 235.218 204.146 222.363 1 32.33 ? O11 3PH 1401 A 1 HETATM 6 C C1 3PH . . . I 3 233.991 203.559 222.749 1 32.33 ? C1 3PH 1401 A 1 HETATM 7 C C2 3PH . . . I 3 233.233 203.585 224.082 1 32.33 ? C2 3PH 1401 A 1 HETATM 8 O O21 3PH . . . I 3 231.869 203.8 223.842 1 32.33 ? O21 3PH 1401 A 1 HETATM 9 C C21 3PH . . . I 3 231.025 203.228 224.829 1 32.33 ? C21 3PH 1401 A 1 HETATM 10 O O22 3PH . . . I 3 230.898 202.052 224.887 1 32.33 ? O22 3PH 1401 A 1 HETATM 11 C C22 3PH . . . I 3 230.271 204.134 225.831 1 32.33 ? C22 3PH 1401 A 1 HETATM 12 C C23 3PH . . . I 3 229.101 203.34 226.466 1 32.33 ? C23 3PH 1401 A 1 HETATM 13 C C24 3PH . . . I 3 229.528 202.806 227.86 1 32.33 ? C24 3PH 1401 A 1 HETATM 14 C C25 3PH . . . I 3 229.432 203.952 228.908 1 32.33 ? C25 3PH 1401 A 1 HETATM 15 C C26 3PH . . . I 3 227.964 204.066 229.41 1 32.33 ? C26 3PH 1401 A 1 HETATM 16 C C27 3PH . . . I 3 227.866 203.569 230.88 1 32.33 ? C27 3PH 1401 A 1 HETATM 17 C C28 3PH . . . I 3 228.397 204.661 231.85 1 32.33 ? C28 3PH 1401 A 1 HETATM 18 C C29 3PH . . . I 3 227.635 204.546 233.196 1 32.33 ? C29 3PH 1401 A 1 HETATM 19 C C2A 3PH . . . I 3 228.504 205.126 234.344 1 32.33 ? C2A 3PH 1401 A 1 HETATM 20 C C2B 3PH . . . I 3 227.575 205.714 235.441 1 32.33 ? C2B 3PH 1401 A 1 HETATM 21 C C2C 3PH . . . I 3 228.165 205.433 236.85 1 32.33 ? C2C 3PH 1401 A 1 HETATM 22 C C2D 3PH . . . I 3 227.25 204.433 237.61 1 32.33 ? C2D 3PH 1401 A 1 HETATM 23 C C2E 3PH . . . I 3 227.723 204.324 239.086 1 32.33 ? C2E 3PH 1401 A 1 HETATM 24 C C2F 3PH . . . I 3 226.617 203.639 239.932 1 32.33 ? C2F 3PH 1401 A 1 HETATM 25 C C3 3PH . . . I 3 233.797 204.711 224.955 1 32.33 ? C3 3PH 1401 A 1 HETATM 26 O O31 3PH . . . I 3 234.638 204.16 225.949 1 32.33 ? O31 3PH 1401 A 1 HETATM 27 C C31 3PH . . . I 3 234.702 204.933 227.129 1 32.33 ? C31 3PH 1401 A 1 HETATM 28 O O32 3PH . . . I 3 234.802 206.113 227.056 1 32.33 ? O32 3PH 1401 A 1 HETATM 29 C C32 3PH . . . I 3 234.64 204.252 228.514 1 32.33 ? C32 3PH 1401 A 1 HETATM 30 C C33 3PH . . . I 3 233.905 205.179 229.514 1 32.33 ? C33 3PH 1401 A 1 HETATM 31 C C34 3PH . . . I 3 233.42 204.345 230.731 1 32.33 ? C34 3PH 1401 A 1 HETATM 32 C C35 3PH . . . I 3 234.113 204.848 232.026 1 32.33 ? C35 3PH 1401 A 1 HETATM 33 C C36 3PH . . . I 3 233.046 205.041 233.136 1 32.33 ? C36 3PH 1401 A 1 HETATM 34 C C37 3PH . . . I 3 233.653 204.664 234.516 1 32.33 ? C37 3PH 1401 A 1 HETATM 35 C C38 3PH . . . I 3 233.402 205.813 235.529 1 32.33 ? C38 3PH 1401 A 1 HETATM 36 C C39 3PH . . . I 3 233.207 205.219 236.951 1 32.33 ? C39 3PH 1401 A 1 HETATM 37 C C3A 3PH . . . I 3 233.488 206.32 238.012 1 32.33 ? C3A 3PH 1401 A 1 HETATM 38 C C3B 3PH . . . I 3 234.466 205.79 239.097 1 32.33 ? C3B 3PH 1401 A 1 HETATM 39 C C3C 3PH . . . I 3 235.717 205.165 238.419 1 32.33 ? C3C 3PH 1401 A 1 HETATM 40 C C3D 3PH . . . I 3 237.01 205.814 238.992 1 32.33 ? C3D 3PH 1401 A 1 HETATM 41 C C3E 3PH . . . I 3 238.263 205.304 238.221 1 32.33 ? C3E 3PH 1401 A 1 HETATM 42 C C3F 3PH . . . I 3 238.003 205.322 236.687 1 32.33 ? C3F 3PH 1401 A 1 HETATM 43 C C3G 3PH . . . I 3 238.156 206.768 236.143 1 32.33 ? C3G 3PH 1401 A 1 HETATM 44 C C3H 3PH . . . I 3 237.654 206.818 234.678 1 32.33 ? C3H 3PH 1401 A 1 HETATM 45 C C3I 3PH . . . I 3 237.784 208.259 234.134 1 32.33 ? C3I 3PH 1401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 45 #