data_5YK6 # _model_server_result.job_id J2uJYHcY6veSmD9KqzsrDA _model_server_result.datetime_utc '2024-11-23 11:57:42' _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 5yk6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5YK6 # _exptl.entry_id 5YK6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 704.998 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5YK6 _cell.length_a 125.504 _cell.length_b 125.504 _cell.length_c 60.875 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YK6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_557 x-y,-y,-z+7/3 1 0 0 0 -1 0 0 0 -1 0 0 142.041667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 5YK6 _atom_sites.fract_transf_matrix[1][1] 0.007968 _atom_sites.fract_transf_matrix[1][2] 0.0046 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009201 _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] 0.016427 _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 B 2 3PH A 1 501 1 3PH 3PH . C 2 3PH A 1 502 1 3PH 3PH . D 3 HOH A 1 601 4 HOH HOH . D 3 HOH A 2 602 1 HOH HOH . D 3 HOH A 3 603 2 HOH HOH . D 3 HOH A 4 604 7 HOH HOH . D 3 HOH A 5 605 6 HOH HOH . D 3 HOH A 6 606 10 HOH HOH . D 3 HOH A 7 607 13 HOH HOH . D 3 HOH A 8 608 8 HOH HOH . D 3 HOH A 9 609 5 HOH HOH . D 3 HOH A 10 610 9 HOH HOH . D 3 HOH A 11 611 12 HOH HOH . D 3 HOH A 12 612 11 HOH HOH . D 3 HOH A 13 613 3 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 O O13 3PH . . . C 2 58.674 3.271 79.194 1 118.7 ? O13 3PH 502 A 1 HETATM 2 P P 3PH . . . C 2 57.592 3.053 80.219 1 136.52 ? P 3PH 502 A 1 HETATM 3 O O14 3PH . . . C 2 57.697 4.096 81.303 1 141.74 ? O14 3PH 502 A 1 HETATM 4 O O12 3PH . . . C 2 57.771 1.675 80.832 1 137.97 ? O12 3PH 502 A 1 HETATM 5 O O11 3PH . . . C 2 56.162 3.161 79.537 1 106.22 ? O11 3PH 502 A 1 HETATM 6 C C1 3PH . . . C 2 55.272 2.017 79.531 1 112.97 ? C1 3PH 502 A 1 HETATM 7 C C2 3PH . . . C 2 53.819 2.428 79.802 1 108.63 ? C2 3PH 502 A 1 HETATM 8 O O21 3PH . . . C 2 53.117 2.532 78.586 1 112.55 ? O21 3PH 502 A 1 HETATM 9 C C21 3PH . . . C 2 51.684 2.582 78.643 1 104.77 ? C21 3PH 502 A 1 HETATM 10 O O22 3PH . . . C 2 51.07 2.872 79.681 1 93.08 ? O22 3PH 502 A 1 HETATM 11 C C22 3PH . . . C 2 50.877 2.27 77.364 1 97.05 ? C22 3PH 502 A 1 HETATM 12 C C23 3PH . . . C 2 49.491 2.924 77.47 1 95.7 ? C23 3PH 502 A 1 HETATM 13 C C24 3PH . . . C 2 48.543 2.253 76.4 1 104.75 ? C24 3PH 502 A 1 HETATM 14 C C25 3PH . . . C 2 48.724 2.964 75.059 1 101.63 ? C25 3PH 502 A 1 HETATM 15 C C26 3PH . . . C 2 48.408 1.967 73.9 1 56.63 ? C26 3PH 502 A 1 HETATM 16 C C27 3PH . . . C 2 46.965 2.235 73.36 1 100.31 ? C27 3PH 502 A 1 HETATM 17 C C28 3PH . . . C 2 46.674 1.266 72.215 1 103.24 ? C28 3PH 502 A 1 HETATM 18 C C3 3PH . . . C 2 53.82 3.761 80.537 1 108.01 ? C3 3PH 502 A 1 HETATM 19 O O31 3PH . . . C 2 53.635 4.837 79.639 1 100.01 ? O31 3PH 502 A 1 HETATM 20 C C31 3PH . . . C 2 53.639 6.07 80.331 1 99.66 ? C31 3PH 502 A 1 HETATM 21 O O32 3PH . . . C 2 54.508 6.325 81.13 1 94.7 ? O32 3PH 502 A 1 HETATM 22 C C32 3PH . . . C 2 52.514 7.075 80.078 1 89.24 ? C32 3PH 502 A 1 HETATM 23 C C33 3PH . . . C 2 51.94 7.486 81.445 1 66.42 ? C33 3PH 502 A 1 HETATM 24 C C34 3PH . . . C 2 50.879 8.607 81.242 1 81.77 ? C34 3PH 502 A 1 HETATM 25 C C35 3PH . . . C 2 49.915 8.219 80.097 1 86.58 ? C35 3PH 502 A 1 HETATM 26 C C36 3PH . . . C 2 48.926 7.135 80.588 1 83.18 ? C36 3PH 502 A 1 HETATM 27 C C37 3PH . . . C 2 47.491 7.558 80.193 1 82.52 ? C37 3PH 502 A 1 HETATM 28 C C38 3PH . . . C 2 46.932 6.6 79.094 1 87.02 ? C38 3PH 502 A 1 HETATM 29 C C39 3PH . . . C 2 46.668 7.371 77.759 1 85.34 ? C39 3PH 502 A 1 HETATM 30 C C3A 3PH . . . C 2 46.639 6.357 76.597 1 98.56 ? C3A 3PH 502 A 1 HETATM 31 C C3B 3PH . . . C 2 45.923 6.957 75.35 1 94.93 ? C3B 3PH 502 A 1 HETATM 32 C C3C 3PH . . . C 2 46.9 7.824 74.54 1 89.73 ? C3C 3PH 502 A 1 HETATM 33 C C3D 3PH . . . C 2 46.306 8.102 73.16 1 92.86 ? C3D 3PH 502 A 1 HETATM 34 C C3E 3PH . . . C 2 45.989 6.752 72.479 1 91.33 ? C3E 3PH 502 A 1 HETATM 35 C C3F 3PH . . . C 2 44.613 6.825 71.791 1 94.96 ? C3F 3PH 502 A 1 HETATM 36 C C3G 3PH . . . C 2 43.688 5.724 72.357 1 92.3 ? C3G 3PH 502 A 1 HETATM 37 C C3H 3PH . . . C 2 43.314 4.693 71.257 1 73.37 ? C3H 3PH 502 A 1 HETATM 38 C C3I 3PH . . . C 2 44.539 3.867 70.847 1 83.19 ? C3I 3PH 502 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #