data_8YHQ # _model_server_result.job_id 4gFCMDCSX6nondtnZfsNRg _model_server_result.datetime_utc '2024-12-26 13:11:48' _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 8yhq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"MA","auth_seq_id":402}' # _entry.id 8YHQ # _exptl.entry_id 8YHQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 564.732 _entity.id 18 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' _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 90 _cell.entry_id 8YHQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YHQ _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 18 DA N N ? 18 MA 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 disulf ? disulf1 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _chem_comp.formula 'C29 H57 O8 P' _chem_comp.formula_weight 564.732 _chem_comp.id 7PH _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' _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 O11 P 7PH sing 101 n n O14 P 7PH doub 102 n n P O13 7PH sing 103 n n P O12 7PH sing 104 n n O12 HO12 7PH sing 105 n n O13 HO13 7PH sing 106 n n C1 O11 7PH sing 107 n n C2 C1 7PH sing 108 n n C1 H1 7PH sing 109 n n C1 H1A 7PH sing 110 n n C3 C2 7PH sing 111 n n C2 O21 7PH sing 112 n n C2 H2 7PH sing 113 n n O31 C3 7PH sing 114 n n C3 H3 7PH sing 115 n n C3 H3A 7PH sing 116 n n C31 O31 7PH sing 117 n n C31 O32 7PH doub 118 n n C32 C31 7PH sing 119 n n C33 C32 7PH sing 120 n n C32 H32 7PH sing 121 n n C32 H32A 7PH sing 122 n n C33 C34 7PH sing 123 n n C33 H33 7PH sing 124 n n C33 H33A 7PH sing 125 n n C34 C35 7PH sing 126 n n C34 H34 7PH sing 127 n n C34 H34A 7PH sing 128 n n C35 C36 7PH sing 129 n n C35 H35 7PH sing 130 n n C35 H35A 7PH sing 131 n n C36 C37 7PH sing 132 n n C36 H36 7PH sing 133 n n C36 H36A 7PH sing 134 n n C37 C38 7PH sing 135 n n C37 H37 7PH sing 136 n n C37 H37A 7PH sing 137 n n C38 C39 7PH sing 138 n n C38 H38 7PH sing 139 n n C38 H38A 7PH sing 140 n n C39 C3A 7PH sing 141 n n C39 H39 7PH sing 142 n n C39 H39A 7PH sing 143 n n C3A C3B 7PH sing 144 n n C3A H3AA 7PH sing 145 n n C3A H3AB 7PH sing 146 n n C3B C3C 7PH sing 147 n n C3B H3B 7PH sing 148 n n C3B H3BA 7PH sing 149 n n C3C H3C 7PH sing 150 n n C3C H3CA 7PH sing 151 n n C3C H3CB 7PH sing 152 n n C21 O21 7PH sing 153 n n O22 C21 7PH doub 154 n n C21 C22 7PH sing 155 n n C23 C22 7PH sing 156 n n C22 H22 7PH sing 157 n n C22 H22A 7PH sing 158 n n C24 C23 7PH sing 159 n n C23 H23 7PH sing 160 n n C23 H23A 7PH sing 161 n n C25 C24 7PH sing 162 n n C24 H24 7PH sing 163 n n C24 H24A 7PH sing 164 n n C26 C25 7PH sing 165 n n C25 H25 7PH sing 166 n n C25 H25A 7PH sing 167 n n C27 C26 7PH sing 168 n n C26 H26 7PH sing 169 n n C26 H26A 7PH sing 170 n n C27 C28 7PH sing 171 n n C27 H27 7PH sing 172 n n C27 H27A 7PH sing 173 n n C28 C29 7PH sing 174 n n C28 H28 7PH sing 175 n n C28 H28A 7PH sing 176 n n C29 C2A 7PH sing 177 n n C29 H29 7PH sing 178 n n C29 H29A 7PH sing 179 n n C2A C2B 7PH sing 180 n n C2A H2A 7PH sing 181 n n C2A H2AA 7PH sing 182 n n C2B C2C 7PH sing 183 n n C2B H2B 7PH sing 184 n n C2B H2BA 7PH sing 185 n n C2C C2D 7PH sing 186 n n C2C H2C 7PH sing 187 n n C2C H2CA 7PH sing 188 n n C2D C2E 7PH sing 189 n n C2D H2D 7PH sing 190 n n C2D H2DA 7PH sing 191 n n C2E H2E 7PH sing 192 n n C2E H2EA 7PH sing 193 n n C2E H2EB 7PH sing 194 n n # _atom_sites.entry_id 8YHQ _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 U 11 6PH C 1 401 402 6PH 6PH . V 12 9PE C 1 402 403 9PE 9PE . W 13 HEM C 1 403 404 HEM HEM . X 13 HEM C 1 404 405 HEM HEM . Y 14 8PE C 1 405 406 8PE 8PE . Z 15 CN5 C 1 406 407 CN5 CN5 . AA 16 UQ6 C 1 407 408 UQ6 UQ6 . BA 17 A1D6K C 1 408 401 A1D6K A1D . CA 13 HEM D 1 401 402 HEM HEM . DA 18 7PH D 1 402 401 7PH 7PH . EA 16 UQ6 L 1 401 402 UQ6 UQ6 . FA 12 9PE L 1 402 403 9PE 9PE . GA 13 HEM L 1 403 404 HEM HEM . HA 19 CN3 L 1 404 405 CN3 CN3 . IA 13 HEM L 1 405 406 HEM HEM . JA 17 A1D6K L 1 406 401 A1D6K A1D . KA 13 HEM M 1 401 401 HEM HEM . LA 11 6PH N 1 401 401 6PH 6PH . MA 18 7PH N 1 402 402 7PH 7PH . NA 14 8PE Q 1 101 101 8PE 8PE . # 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 P P 7PH . . . MA 18 137.389 163.464 106.315 1 22.54 ? P 7PH 402 N 1 HETATM 2 O O12 7PH . . . MA 18 136.52 162.765 105.302 1 22.54 ? O12 7PH 402 N 1 HETATM 3 O O13 7PH . . . MA 18 138.23 164.505 105.623 1 22.54 ? O13 7PH 402 N 1 HETATM 4 O O14 7PH . . . MA 18 136.507 164.137 107.333 1 22.54 ? O14 7PH 402 N 1 HETATM 5 O O11 7PH . . . MA 18 138.347 162.357 107.066 1 22.54 ? O11 7PH 402 N 1 HETATM 6 C C1 7PH . . . MA 18 139.734 162.444 106.945 1 22.54 ? C1 7PH 402 N 1 HETATM 7 C C2 7PH . . . MA 18 140.399 161.758 108.135 1 22.54 ? C2 7PH 402 N 1 HETATM 8 C C3 7PH . . . MA 18 140.372 162.65 109.376 1 22.54 ? C3 7PH 402 N 1 HETATM 9 O O31 7PH . . . MA 18 141.486 162.371 110.175 1 22.54 ? O31 7PH 402 N 1 HETATM 10 O O32 7PH . . . MA 18 140.427 162.722 112.129 1 22.54 ? O32 7PH 402 N 1 HETATM 11 C C31 7PH . . . MA 18 141.219 162.089 111.519 1 22.54 ? C31 7PH 402 N 1 HETATM 12 C C32 7PH . . . MA 18 141.977 160.963 112.208 1 22.54 ? C32 7PH 402 N 1 HETATM 13 C C33 7PH . . . MA 18 141.004 159.899 112.702 1 22.54 ? C33 7PH 402 N 1 HETATM 14 C C34 7PH . . . MA 18 141.633 159.116 113.857 1 22.54 ? C34 7PH 402 N 1 HETATM 15 C C35 7PH . . . MA 18 141.332 159.729 115.224 1 22.54 ? C35 7PH 402 N 1 HETATM 16 C C36 7PH . . . MA 18 140.975 158.64 116.233 1 22.54 ? C36 7PH 402 N 1 HETATM 17 C C37 7PH . . . MA 18 139.553 158.118 116.029 1 22.54 ? C37 7PH 402 N 1 HETATM 18 C C38 7PH . . . MA 18 139.24 157.073 117.1 1 22.54 ? C38 7PH 402 N 1 HETATM 19 C C39 7PH . . . MA 18 138.665 155.773 116.515 1 22.54 ? C39 7PH 402 N 1 HETATM 20 C C3A 7PH . . . MA 18 137.167 155.894 116.217 1 22.54 ? C3A 7PH 402 N 1 HETATM 21 C C3B 7PH . . . MA 18 136.432 154.558 116.325 1 22.54 ? C3B 7PH 402 N 1 HETATM 22 C C3C 7PH . . . MA 18 134.992 154.801 116.765 1 22.54 ? C3C 7PH 402 N 1 HETATM 23 O O21 7PH . . . MA 18 139.706 160.576 108.435 1 22.54 ? O21 7PH 402 N 1 HETATM 24 O O22 7PH . . . MA 18 140.933 159.39 106.957 1 22.54 ? O22 7PH 402 N 1 HETATM 25 C C21 7PH . . . MA 18 140.106 159.392 107.801 1 22.54 ? C21 7PH 402 N 1 HETATM 26 C C22 7PH . . . MA 18 139.442 158.085 108.229 1 22.54 ? C22 7PH 402 N 1 HETATM 27 C C23 7PH . . . MA 18 140.399 156.903 108.117 1 22.54 ? C23 7PH 402 N 1 HETATM 28 C C24 7PH . . . MA 18 141.307 156.869 109.336 1 22.54 ? C24 7PH 402 N 1 HETATM 29 C C25 7PH . . . MA 18 142.719 156.428 108.991 1 22.54 ? C25 7PH 402 N 1 HETATM 30 C C26 7PH . . . MA 18 143.598 156.903 110.136 1 22.54 ? C26 7PH 402 N 1 HETATM 31 C C27 7PH . . . MA 18 144.944 156.186 110.164 1 22.54 ? C27 7PH 402 N 1 HETATM 32 C C28 7PH . . . MA 18 145.435 156.044 111.604 1 22.54 ? C28 7PH 402 N 1 HETATM 33 C C29 7PH . . . MA 18 145.109 154.691 112.237 1 22.54 ? C29 7PH 402 N 1 HETATM 34 C C2A 7PH . . . MA 18 143.798 154.694 113.02 1 22.54 ? C2A 7PH 402 N 1 HETATM 35 C C2B 7PH . . . MA 18 142.982 153.461 112.666 1 22.54 ? C2B 7PH 402 N 1 HETATM 36 C C2C 7PH . . . MA 18 141.656 153.463 113.416 1 22.54 ? C2C 7PH 402 N 1 HETATM 37 C C2D 7PH . . . MA 18 140.658 152.613 112.634 1 22.54 ? C2D 7PH 402 N 1 HETATM 38 C C2E 7PH . . . MA 18 139.616 151.991 113.56 1 22.54 ? C2E 7PH 402 N 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #