data_5YK6 # _model_server_result.job_id irBbv0I32vGy28orROVYcw _model_server_result.datetime_utc '2024-11-23 12:42:55' _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":"B","auth_seq_id":501}' # _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 . . . B 2 61.382 15.659 76.023 1 86.35 ? O13 3PH 501 A 1 HETATM 2 P P 3PH . . . B 2 60.689 16.734 76.825 1 79.28 ? P 3PH 501 A 1 HETATM 3 O O14 3PH . . . B 2 59.293 16.982 76.322 1 74.09 ? O14 3PH 501 A 1 HETATM 4 O O12 3PH . . . B 2 61.492 18.025 76.727 1 75.59 ? O12 3PH 501 A 1 HETATM 5 O O11 3PH . . . B 2 60.565 16.265 78.329 1 104.49 ? O11 3PH 501 A 1 HETATM 6 C C1 3PH . . . B 2 60.066 17.233 79.273 1 97.65 ? C1 3PH 501 A 1 HETATM 7 C C2 3PH . . . B 2 59.114 16.595 80.283 1 91.24 ? C2 3PH 501 A 1 HETATM 8 O O21 3PH . . . B 2 58.377 17.621 80.902 1 79.24 ? O21 3PH 501 A 1 HETATM 9 C C21 3PH . . . B 2 57.016 17.315 81.205 1 81.08 ? C21 3PH 501 A 1 HETATM 10 O O22 3PH . . . B 2 56.504 16.256 80.798 1 82.67 ? O22 3PH 501 A 1 HETATM 11 C C22 3PH . . . B 2 56.208 18.339 82.043 1 64.12 ? C22 3PH 501 A 1 HETATM 12 C C23 3PH . . . B 2 54.744 17.901 82.224 1 68.6 ? C23 3PH 501 A 1 HETATM 13 C C24 3PH . . . B 2 53.94 19.078 82.906 1 70.27 ? C24 3PH 501 A 1 HETATM 14 C C25 3PH . . . B 2 52.789 18.498 83.738 1 80.75 ? C25 3PH 501 A 1 HETATM 15 C C26 3PH . . . B 2 51.813 17.708 82.807 1 144.73 ? C26 3PH 501 A 1 HETATM 16 C C27 3PH . . . B 2 50.336 18.129 83.117 1 88.13 ? C27 3PH 501 A 1 HETATM 17 C C28 3PH . . . B 2 49.431 16.902 83.041 1 90.69 ? C28 3PH 501 A 1 HETATM 18 C C29 3PH . . . B 2 48.17 17.23 82.23 1 78.33 ? C29 3PH 501 A 1 HETATM 19 C C2A 3PH . . . B 2 47.203 16.028 82.327 1 78.32 ? C2A 3PH 501 A 1 HETATM 20 C C2B 3PH . . . B 2 46.461 15.854 80.957 1 76.68 ? C2B 3PH 501 A 1 HETATM 21 C C2C 3PH . . . B 2 47.54 15.76 79.814 1 73.59 ? C2C 3PH 501 A 1 HETATM 22 C C2D 3PH . . . B 2 47.103 14.736 78.759 1 68.68 ? C2D 3PH 501 A 1 HETATM 23 C C2E 3PH . . . B 2 48.346 14.365 77.912 1 73.46 ? C2E 3PH 501 A 1 HETATM 24 C C2F 3PH . . . B 2 48.069 13.072 77.213 1 72.01 ? C2F 3PH 501 A 1 HETATM 25 C C2G 3PH . . . B 2 48.816 11.921 77.917 1 63.02 ? C2G 3PH 501 A 1 HETATM 26 C C2H 3PH . . . B 2 48.409 10.605 77.272 1 64.51 ? C2H 3PH 501 A 1 HETATM 27 C C2I 3PH . . . B 2 48.134 10.817 75.78 1 56.51 ? C2I 3PH 501 A 1 HETATM 28 C C3 3PH . . . B 2 59.909 15.824 81.331 1 91.07 ? C3 3PH 501 A 1 HETATM 29 O O31 3PH . . . B 2 59.02 15.272 82.287 1 96.68 ? O31 3PH 501 A 1 HETATM 30 C C31 3PH . . . B 2 58.825 13.872 82.182 1 104.45 ? C31 3PH 501 A 1 HETATM 31 O O32 3PH . . . B 2 58.832 13.337 81.106 1 114.67 ? O32 3PH 501 A 1 HETATM 32 C C32 3PH . . . B 2 58.613 13.037 83.454 1 101.79 ? C32 3PH 501 A 1 HETATM 33 C C33 3PH . . . B 2 57.933 11.686 83.142 1 103.23 ? C33 3PH 501 A 1 HETATM 34 C C34 3PH . . . B 2 56.465 11.927 82.671 1 94.55 ? C34 3PH 501 A 1 HETATM 35 C C35 3PH . . . B 2 55.464 11.898 83.852 1 83.41 ? C35 3PH 501 A 1 HETATM 36 C C36 3PH . . . B 2 55.318 13.309 84.458 1 79.38 ? C36 3PH 501 A 1 HETATM 37 C C37 3PH . . . B 2 53.83 13.658 84.706 1 80.16 ? C37 3PH 501 A 1 HETATM 38 C C38 3PH . . . B 2 53.175 12.583 85.624 1 63.1 ? C38 3PH 501 A 1 HETATM 39 C C39 3PH . . . B 2 51.659 12.428 85.267 1 90.59 ? C39 3PH 501 A 1 HETATM 40 C C3A 3PH . . . B 2 51.019 13.814 85.064 1 88.18 ? C3A 3PH 501 A 1 HETATM 41 C C3B 3PH . . . B 2 49.917 14.033 86.137 1 81.94 ? C3B 3PH 501 A 1 HETATM 42 C C3C 3PH . . . B 2 50.52 14.654 87.405 1 88.45 ? C3C 3PH 501 A 1 HETATM 43 C C3D 3PH . . . B 2 51.548 15.722 87.02 1 98.59 ? C3D 3PH 501 A 1 HETATM 44 C C3E 3PH . . . B 2 50.872 17.11 86.918 1 99.25 ? C3E 3PH 501 A 1 HETATM 45 C C3F 3PH . . . B 2 50.171 17.421 88.25 1 93.88 ? C3F 3PH 501 A 1 HETATM 46 C C3G 3PH . . . B 2 49.306 18.683 88.087 1 94.1 ? C3G 3PH 501 A 1 HETATM 47 C C3H 3PH . . . B 2 50.043 19.894 88.708 1 72.26 ? C3H 3PH 501 A 1 HETATM 48 C C3I 3PH . . . B 2 49.143 21.124 88.612 1 76.87 ? C3I 3PH 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #