data_8YIN # _model_server_result.job_id fNdZsUHLGeykFK14GDzSnw _model_server_result.datetime_utc '2024-12-26 13:09:10' _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 8yin # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IA","auth_seq_id":404}' # _entry.id 8YIN # _exptl.entry_id 8YIN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 593.773 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate' _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 8YIN _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YIN _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 _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 ? 13 W N N ? 13 IA 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 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? disulf ? disulf2 O SG CYS 134 P CYS 164 1_555 O SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 X FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 Y FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 X FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 Y FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc6 G NE2 HIS 82 N HIS 82 1_555 JA FE HEM . N HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc7 G NE2 HIS 96 N HIS 96 1_555 GA FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc8 G NE2 HIS 183 N HIS 183 1_555 JA FE HEM . N HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc9 G NE2 HIS 197 N HIS 197 1_555 GA FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc10 M NE2 HIS 44 O HIS 105 1_555 LA FE HEM . O HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? # _chem_comp.formula 'C30 H60 N O8 P' _chem_comp.formula_weight 593.773 _chem_comp.id 9PE _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-SN-PHOSPHATIDYLETHANOLAMINE # 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 O12 P 9PE doub 221 n n P O11 9PE sing 222 n n P O14 9PE sing 223 n n P O13 9PE sing 224 n n C12 N 9PE sing 225 n n N HN 9PE sing 226 n n N HNA 9PE sing 227 n n O11 C1 9PE sing 228 n n O13 C11 9PE sing 229 n n O14 HO14 9PE sing 230 n n C11 C12 9PE sing 231 n n C11 H11 9PE sing 232 n n C11 H11A 9PE sing 233 n n C12 H12 9PE sing 234 n n C12 H12A 9PE sing 235 n n C2 C1 9PE sing 236 n n C1 H1 9PE sing 237 n n C1 H1A 9PE sing 238 n n O21 C2 9PE sing 239 n n C2 C3 9PE sing 240 n n C2 H2 9PE sing 241 n n O31 C3 9PE sing 242 n n C3 H3 9PE sing 243 n n C3 H3A 9PE sing 244 n n O31 C31 9PE sing 245 n n C31 O32 9PE doub 246 n n C32 C31 9PE sing 247 n n C33 C32 9PE sing 248 n n C32 H32 9PE sing 249 n n C32 H32A 9PE sing 250 n n C34 C33 9PE sing 251 n n C33 H33 9PE sing 252 n n C33 H33A 9PE sing 253 n n C35 C34 9PE sing 254 n n C34 H34 9PE sing 255 n n C34 H34A 9PE sing 256 n n C36 C35 9PE sing 257 n n C35 H35 9PE sing 258 n n C35 H35A 9PE sing 259 n n C37 C36 9PE sing 260 n n C36 H36 9PE sing 261 n n C36 H36A 9PE sing 262 n n C37 H37 9PE sing 263 n n C37 H37A 9PE sing 264 n n C37 H37B 9PE sing 265 n n C21 O21 9PE sing 266 n n O22 C21 9PE doub 267 n n C22 C21 9PE sing 268 n n C23 C22 9PE sing 269 n n C22 H22 9PE sing 270 n n C22 H22A 9PE sing 271 n n C23 C24 9PE sing 272 n n C23 H23 9PE sing 273 n n C23 H23A 9PE sing 274 n n C25 C24 9PE sing 275 n n C24 H24 9PE sing 276 n n C24 H24A 9PE sing 277 n n C26 C25 9PE sing 278 n n C25 H25 9PE sing 279 n n C25 H25A 9PE sing 280 n n C27 C26 9PE sing 281 n n C26 H26 9PE sing 282 n n C26 H26A 9PE sing 283 n n C28 C27 9PE sing 284 n n C27 H27 9PE sing 285 n n C27 H27A 9PE sing 286 n n C28 C29 9PE sing 287 n n C28 H28 9PE sing 288 n n C28 H28A 9PE sing 289 n n C2A C29 9PE sing 290 n n C29 H29 9PE sing 291 n n C29 H29A 9PE sing 292 n n C2A C2B 9PE sing 293 n n C2A H2A 9PE sing 294 n n C2A H2AA 9PE sing 295 n n C2C C2B 9PE sing 296 n n C2B H2B 9PE sing 297 n n C2B H2BA 9PE sing 298 n n C2C C2D 9PE sing 299 n n C2C H2C 9PE sing 300 n n C2C H2CA 9PE sing 301 n n C2E C2D 9PE sing 302 n n C2D H2D 9PE sing 303 n n C2D H2DA 9PE sing 304 n n C2E C2F 9PE sing 305 n n C2E H2E 9PE sing 306 n n C2E H2EA 9PE sing 307 n n C2G C2F 9PE sing 308 n n C2F H2F 9PE sing 309 n n C2F H2FA 9PE sing 310 n n C2H C2G 9PE sing 311 n n C2G H2G 9PE sing 312 n n C2G H2GA 9PE sing 313 n n C2I C2H 9PE sing 314 n n C2H H2H 9PE sing 315 n n C2H H2HA 9PE sing 316 n n C2I H2I 9PE sing 317 n n C2I H2IA 9PE sing 318 n n C2I H2IB 9PE sing 319 n n # _atom_sites.entry_id 8YIN _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 A 1 501 501 6PH 6PH . V 12 CN3 C 1 401 401 CN3 CN3 . W 13 9PE C 1 402 402 9PE 9PE . X 14 HEM C 1 403 403 HEM HEM . Y 14 HEM C 1 404 404 HEM HEM . Z 15 CN5 C 1 405 405 CN5 CN5 . AA 16 UQ6 C 1 406 406 UQ6 UQ6 . BA 17 A1D6O C 1 407 407 A1D6O A1D . CA 14 HEM D 1 401 401 HEM HEM . DA 11 6PH E 1 301 301 6PH 6PH . EA 18 8PE H 1 101 101 8PE 8PE . FA 12 CN3 N 1 401 404 CN3 CN3 . GA 14 HEM N 1 402 405 HEM HEM . HA 16 UQ6 N 1 403 401 UQ6 UQ6 . IA 13 9PE N 1 404 402 9PE 9PE . JA 14 HEM N 1 405 403 HEM HEM . KA 17 A1D6O N 1 406 406 A1D6O A1D . LA 14 HEM O 1 401 401 HEM HEM . MA 18 8PE S 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 9PE . . . IA 13 138.633 168.731 152.111 1 64.64 ? P 9PE 404 N 1 HETATM 2 N N 9PE . . . IA 13 135.25 168.454 149.717 1 64.64 ? N 9PE 404 N 1 HETATM 3 O O11 9PE . . . IA 13 139.008 167.13 152.021 1 64.64 ? O11 9PE 404 N 1 HETATM 4 O O12 9PE . . . IA 13 139.589 169.43 153.046 1 64.64 ? O12 9PE 404 N 1 HETATM 5 O O13 9PE . . . IA 13 137.092 168.875 152.676 1 64.64 ? O13 9PE 404 N 1 HETATM 6 O O14 9PE . . . IA 13 138.741 169.345 150.735 1 64.64 ? O14 9PE 404 N 1 HETATM 7 C C11 9PE . . . IA 13 136.072 168.203 151.995 1 64.64 ? C11 9PE 404 N 1 HETATM 8 C C12 9PE . . . IA 13 135.43 169.145 150.979 1 64.64 ? C12 9PE 404 N 1 HETATM 9 C C1 9PE . . . IA 13 139.749 166.537 153.048 1 64.64 ? C1 9PE 404 N 1 HETATM 10 C C2 9PE . . . IA 13 140.65 165.46 152.449 1 64.64 ? C2 9PE 404 N 1 HETATM 11 C C3 9PE . . . IA 13 139.88 164.719 151.358 1 64.64 ? C3 9PE 404 N 1 HETATM 12 O O31 9PE . . . IA 13 140.147 165.282 150.11 1 64.64 ? O31 9PE 404 N 1 HETATM 13 O O32 9PE . . . IA 13 140.707 163.385 149.068 1 64.64 ? O32 9PE 404 N 1 HETATM 14 C C31 9PE . . . IA 13 140.985 164.508 149.305 1 64.64 ? C31 9PE 404 N 1 HETATM 15 C C32 9PE . . . IA 13 142.256 165.12 148.727 1 64.64 ? C32 9PE 404 N 1 HETATM 16 C C33 9PE . . . IA 13 143.342 164.053 148.677 1 64.64 ? C33 9PE 404 N 1 HETATM 17 C C34 9PE . . . IA 13 144.597 164.648 148.047 1 64.64 ? C34 9PE 404 N 1 HETATM 18 C C35 9PE . . . IA 13 145.056 163.707 146.941 1 64.64 ? C35 9PE 404 N 1 HETATM 19 C C36 9PE . . . IA 13 145.45 164.514 145.71 1 64.64 ? C36 9PE 404 N 1 HETATM 20 C C37 9PE . . . IA 13 144.772 163.898 144.488 1 64.64 ? C37 9PE 404 N 1 HETATM 21 O O21 9PE . . . IA 13 141.791 166.06 151.902 1 64.64 ? O21 9PE 404 N 1 HETATM 22 O O22 9PE . . . IA 13 143.002 165.464 153.702 1 64.64 ? O22 9PE 404 N 1 HETATM 23 C C21 9PE . . . IA 13 142.905 166.156 152.747 1 64.64 ? C21 9PE 404 N 1 HETATM 24 C C22 9PE . . . IA 13 143.993 167.177 152.433 1 64.64 ? C22 9PE 404 N 1 HETATM 25 C C23 9PE . . . IA 13 145.197 166.485 151.8 1 64.64 ? C23 9PE 404 N 1 HETATM 26 C C24 9PE . . . IA 13 146.169 167.548 151.295 1 64.64 ? C24 9PE 404 N 1 HETATM 27 C C25 9PE . . . IA 13 147.592 166.997 151.269 1 64.64 ? C25 9PE 404 N 1 HETATM 28 C C26 9PE . . . IA 13 147.723 165.888 150.228 1 64.64 ? C26 9PE 404 N 1 HETATM 29 C C27 9PE . . . IA 13 149.196 165.736 149.854 1 64.64 ? C27 9PE 404 N 1 HETATM 30 C C28 9PE . . . IA 13 149.414 164.427 149.098 1 64.64 ? C28 9PE 404 N 1 HETATM 31 C C29 9PE . . . IA 13 150.888 164.034 149.176 1 64.64 ? C29 9PE 404 N 1 HETATM 32 C C2A 9PE . . . IA 13 151.106 162.685 148.498 1 64.64 ? C2A 9PE 404 N 1 HETATM 33 C C2B 9PE . . . IA 13 151.035 161.582 149.549 1 64.64 ? C2B 9PE 404 N 1 HETATM 34 C C2C 9PE . . . IA 13 152.127 160.551 149.295 1 64.64 ? C2C 9PE 404 N 1 HETATM 35 C C2D 9PE . . . IA 13 151.472 159.196 149.037 1 64.64 ? C2D 9PE 404 N 1 HETATM 36 C C2E 9PE . . . IA 13 152.463 158.057 149.294 1 64.64 ? C2E 9PE 404 N 1 HETATM 37 C C2F 9PE . . . IA 13 152.968 157.443 147.985 1 64.64 ? C2F 9PE 404 N 1 HETATM 38 C C2G 9PE . . . IA 13 151.819 157.175 147.012 1 64.64 ? C2G 9PE 404 N 1 HETATM 39 C C2H 9PE . . . IA 13 152.225 157.669 145.628 1 64.64 ? C2H 9PE 404 N 1 HETATM 40 C C2I 9PE . . . IA 13 151.335 158.843 145.234 1 64.64 ? C2I 9PE 404 N 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 372 _model_server_stats.encode_time_ms 25 _model_server_stats.element_count 40 #