data_8ABK # _model_server_result.job_id dLEiO6XlULfJBEIMsC63ag _model_server_result.datetime_utc '2025-03-30 16:35:25' _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 8abk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"WA","auth_seq_id":3003}' # _entry.id 8ABK # _exptl.entry_id 8ABK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 591.777 _entity.id 18 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-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 90 _cell.entry_id 8ABK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ABK _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,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB _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 FA N N ? 18 WA 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 B SG CYS 173 P CYS 173 1_555 B SG CYS 189 P CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 D SG CYS 81 F CYS 91 1_555 D SG CYS 123 F CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf3 D SG CYS 91 F CYS 101 1_555 D SG CYS 113 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 N SG CYS 81 Q CYS 91 1_555 N SG CYS 123 Q CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 N SG CYS 91 Q CYS 101 1_555 N SG CYS 113 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc1 A NE2 HIS 82 C HIS 82 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc2 A NE2 HIS 96 C HIS 96 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 A NE2 HIS 183 C HIS 183 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 A NE2 HIS 197 C HIS 197 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc5 B SG CYS 168 P CYS 168 1_555 BA FE1 FES . P FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc6 B ND1 HIS 170 P HIS 170 1_555 BA FE2 FES . P FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc7 B SG CYS 187 P CYS 187 1_555 BA FE1 FES . P FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc8 B ND1 HIS 190 P HIS 190 1_555 BA FE2 FES . P FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc9 G NE2 HIS 128 D HIS 128 1_555 GA FE HEC . D HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc10 G SD MET 248 D MET 248 1_555 GA FE HEC . D HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 K NE2 HIS 82 N HIS 82 1_555 LA FE HEM . N HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc12 K NE2 HIS 96 N HIS 96 1_555 MA FE HEM . N HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc13 K NE2 HIS 183 N HIS 183 1_555 LA FE HEM . N HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc14 K NE2 HIS 197 N HIS 197 1_555 MA FE HEM . N HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc15 Q NE2 HIS 128 O HIS 128 1_555 XA FE HEC . O HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc16 Q SD MET 248 O MET 248 1_555 XA FE HEC . O HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _chem_comp.formula 'C31 H60 O8 P -1' _chem_comp.formula_weight 591.777 _chem_comp.id XP4 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O1 P1 XP4 sing 1204 n n O2 P1 XP4 doub 1205 n n P1 O3 XP4 sing 1206 n n P1 O4 XP4 sing 1207 n n O3 H1 XP4 sing 1208 n n O4 C1 XP4 sing 1209 n n C1 C2 XP4 sing 1210 n n C1 H2 XP4 sing 1211 n n C1 H3 XP4 sing 1212 n n C2 C3 XP4 sing 1213 n n C2 O7 XP4 sing 1214 n n C2 H4 XP4 sing 1215 n n C3 O5 XP4 sing 1216 n n C3 H5 XP4 sing 1217 n n C3 H6 XP4 sing 1218 n n O5 C4 XP4 sing 1219 n n C4 O6 XP4 doub 1220 n n C4 C5 XP4 sing 1221 n n C5 C6 XP4 sing 1222 n n C5 H7 XP4 sing 1223 n n C5 H8 XP4 sing 1224 n n C6 C7 XP4 sing 1225 n n C6 H9 XP4 sing 1226 n n C6 H10 XP4 sing 1227 n n C7 C8 XP4 sing 1228 n n C7 H11 XP4 sing 1229 n n C7 H12 XP4 sing 1230 n n C8 C9 XP4 sing 1231 n n C8 H13 XP4 sing 1232 n n C8 H14 XP4 sing 1233 n n C9 C10 XP4 sing 1234 n n C9 H15 XP4 sing 1235 n n C9 H16 XP4 sing 1236 n n C10 C11 XP4 sing 1237 n n C10 H17 XP4 sing 1238 n n C10 H18 XP4 sing 1239 n n C11 C12 XP4 sing 1240 n n C11 H19 XP4 sing 1241 n n C11 H20 XP4 sing 1242 n n C12 C13 XP4 sing 1243 n n C12 H21 XP4 sing 1244 n n C12 H22 XP4 sing 1245 n n C13 C14 XP4 sing 1246 n n C13 H23 XP4 sing 1247 n n C13 H24 XP4 sing 1248 n n C14 C15 XP4 sing 1249 n n C14 H25 XP4 sing 1250 n n C14 H26 XP4 sing 1251 n n C15 C16 XP4 sing 1252 n n C15 H27 XP4 sing 1253 n n C15 H28 XP4 sing 1254 n n C16 C17 XP4 sing 1255 n n C16 H29 XP4 sing 1256 n n C16 H30 XP4 sing 1257 n n C17 H31 XP4 sing 1258 n n C17 H32 XP4 sing 1259 n n C17 H33 XP4 sing 1260 n n O7 C18 XP4 sing 1261 n n C18 O8 XP4 doub 1262 n n C18 C19 XP4 sing 1263 n n C19 C20 XP4 sing 1264 n n C19 H34 XP4 sing 1265 n n C19 H35 XP4 sing 1266 n n C20 C21 XP4 sing 1267 n n C20 H36 XP4 sing 1268 n n C20 H37 XP4 sing 1269 n n C21 C22 XP4 sing 1270 n n C21 H38 XP4 sing 1271 n n C21 H39 XP4 sing 1272 n n C22 C23 XP4 sing 1273 n n C22 H40 XP4 sing 1274 n n C22 H41 XP4 sing 1275 n n C23 C24 XP4 sing 1276 n n C23 H42 XP4 sing 1277 n n C23 H43 XP4 sing 1278 n n C24 C25 XP4 sing 1279 n n C24 H44 XP4 sing 1280 n n C24 H45 XP4 sing 1281 n n C25 C26 XP4 sing 1282 n n C25 H46 XP4 sing 1283 n n C25 H47 XP4 sing 1284 n n C26 C27 XP4 sing 1285 n n C26 H48 XP4 sing 1286 n n C26 H49 XP4 sing 1287 n n C27 C28 XP4 sing 1288 n n C27 H50 XP4 sing 1289 n n C27 H51 XP4 sing 1290 n n C28 C29 XP4 sing 1291 n n C28 H52 XP4 sing 1292 n n C28 H53 XP4 sing 1293 n n C29 C30 XP4 sing 1294 n n C29 H54 XP4 sing 1295 n n C29 H55 XP4 sing 1296 n n C30 C31 XP4 sing 1297 n n C30 H56 XP4 sing 1298 n n C30 H57 XP4 sing 1299 n n C31 H58 XP4 sing 1300 n n C31 H59 XP4 sing 1301 n n C31 H60 XP4 sing 1302 n n # _atom_sites.entry_id 8ABK _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 HEM C 1 501 501 HEM HEM . V 11 HEM C 1 502 502 HEM HEM . W 12 PC1 C 1 503 503 PC1 PC1 . X 13 PTY C 1 504 504 PTY PTY . Y 14 CDL C 1 505 505 CDL CDL . Z 15 DCQ C 1 506 506 DCQ DCQ . AA 16 LMT C 1 507 507 LMT LMT . BA 17 FES P 1 301 301 FES FES . CA 13 PTY P 1 302 302 PTY PTY . DA 14 CDL A 1 3001 3001 CDL CDL . EA 14 CDL A 1 3002 3002 CDL CDL . FA 18 XP4 A 1 3003 3003 XP4 XP4 . GA 19 HEC D 1 401 401 HEC HEC . HA 14 CDL H 1 701 701 CDL CDL . IA 14 CDL H 1 702 702 CDL CDL . JA 12 PC1 I 1 201 201 PC1 PC1 . KA 16 LMT J 1 101 101 LMT LMT . LA 11 HEM N 1 501 501 HEM HEM . MA 11 HEM N 1 502 502 HEM HEM . NA 12 PC1 N 1 503 503 PC1 PC1 . OA 14 CDL N 1 504 504 CDL CDL . PA 13 PTY N 1 505 505 PTY PTY . QA 14 CDL N 1 506 506 CDL CDL . RA 15 DCQ N 1 507 507 DCQ DCQ . SA 16 LMT N 1 508 508 LMT LMT . TA 13 PTY E 1 401 401 PTY PTY . UA 14 CDL L 1 3001 3001 CDL CDL . VA 14 CDL L 1 3002 3002 CDL CDL . WA 18 XP4 L 1 3003 3003 XP4 XP4 . XA 19 HEC O 1 401 401 HEC HEC . YA 14 CDL S 1 101 101 CDL CDL . ZA 12 PC1 T 1 201 201 PC1 PC1 . AB 16 LMT U 1 101 101 LMT LMT . # 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 O1 XP4 . . . WA 18 120.188 155.706 160.191 1 72.75 ? O1 XP4 3003 L 1 HETATM 2 O O2 XP4 . . . WA 18 120.006 158.187 160.736 1 68.8 ? O2 XP4 3003 L 1 HETATM 3 P P1 XP4 . . . WA 18 120.393 157.135 159.729 1 71.56 ? P1 XP4 3003 L 1 HETATM 4 O O3 XP4 . . . WA 18 121.728 157.392 159.069 1 76.33 ? O3 XP4 3003 L 1 HETATM 5 O O4 XP4 . . . WA 18 119.295 157.421 158.584 1 70.92 ? O4 XP4 3003 L 1 HETATM 6 C C1 XP4 . . . WA 18 118.879 156.461 157.614 1 65.73 ? C1 XP4 3003 L 1 HETATM 7 C C2 XP4 . . . WA 18 118.929 156.993 156.184 1 60.34 ? C2 XP4 3003 L 1 HETATM 8 C C3 XP4 . . . WA 18 120.252 157.637 155.918 1 53.81 ? C3 XP4 3003 L 1 HETATM 9 O O5 XP4 . . . WA 18 120.131 158.023 154.557 1 50.37 ? O5 XP4 3003 L 1 HETATM 10 C C4 XP4 . . . WA 18 121.299 158.402 153.815 1 52.95 ? C4 XP4 3003 L 1 HETATM 11 O O6 XP4 . . . WA 18 122.352 158.406 154.422 1 53.86 ? O6 XP4 3003 L 1 HETATM 12 C C5 XP4 . . . WA 18 121.162 158.819 152.372 1 54.97 ? C5 XP4 3003 L 1 HETATM 13 C C6 XP4 . . . WA 18 122.508 158.904 151.684 1 60.25 ? C6 XP4 3003 L 1 HETATM 14 C C7 XP4 . . . WA 18 122.316 159.395 150.253 1 67.93 ? C7 XP4 3003 L 1 HETATM 15 C C8 XP4 . . . WA 18 123.568 160.119 149.707 1 72.35 ? C8 XP4 3003 L 1 HETATM 16 C C9 XP4 . . . WA 18 123.613 160.153 148.162 1 78.46 ? C9 XP4 3003 L 1 HETATM 17 C C10 XP4 . . . WA 18 124.746 160.905 147.441 1 80.74 ? C10 XP4 3003 L 1 HETATM 18 C C11 XP4 . . . WA 18 124.482 160.861 145.911 1 85.04 ? C11 XP4 3003 L 1 HETATM 19 C C12 XP4 . . . WA 18 125.33 161.807 145.035 1 91.17 ? C12 XP4 3003 L 1 HETATM 20 C C13 XP4 . . . WA 18 124.755 162.203 143.649 1 92.24 ? C13 XP4 3003 L 1 HETATM 21 O O7 XP4 . . . WA 18 119.021 155.823 155.328 1 62.31 ? O7 XP4 3003 L 1 HETATM 22 C C18 XP4 . . . WA 18 117.819 155.109 154.903 1 59.6 ? C18 XP4 3003 L 1 HETATM 23 O O8 XP4 . . . WA 18 116.781 155.67 155.181 1 62.52 ? O8 XP4 3003 L 1 HETATM 24 C C19 XP4 . . . WA 18 117.85 153.779 154.13 1 57.82 ? C19 XP4 3003 L 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #