data_8D1L # _model_server_result.job_id jY-XIISK8VmkA8g-aSV3Pw _model_server_result.datetime_utc '2025-04-03 11:04:49' _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 8d1l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":608}' # _entry.id 8D1L # _exptl.entry_id 8D1L _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 677.933 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 40 _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 8D1L _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D1L _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 CA N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 IA N N ? 3 JA N N ? 3 KA N N ? 3 LA N N ? 3 MA N N ? 3 NA N N ? 3 OA N N ? 3 PA N N ? 3 QA N N ? 3 SA N N ? 3 TA N N ? 3 UA N N ? 3 VA N N ? 3 WA N N ? 3 XA N N ? 3 YA 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 metalc ? metalc1 A O ALA 10 B ALA 10 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc2 A O GLN 293 B GLN 293 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc3 A O ASN 296 B ASN 296 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc4 A OD2 ASP 301 B ASP 301 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc5 A OD1 ASP 304 B ASP 304 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc6 A OD2 ASP 304 B ASP 304 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc7 F CA CA . B CA 601 1_555 C O ALA 10 A ALA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc8 B O ALA 10 C ALA 10 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc9 B O GLN 293 C GLN 293 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc10 B O ASN 296 C ASN 296 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc11 B OD2 ASP 301 C ASP 301 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc12 B OD1 ASP 304 C ASP 304 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc13 B OD2 ASP 304 C ASP 304 1_555 O CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc14 C O GLN 293 A GLN 293 1_555 Y CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc15 C O ASN 296 A ASN 296 1_555 Y CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc16 C OD2 ASP 301 A ASP 301 1_555 Y CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc17 C OD1 ASP 304 A ASP 304 1_555 Y CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc18 C OD2 ASP 304 A ASP 304 1_555 Y CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc19 Y CA CA . A CA 602 1_555 E O ALA 10 E ALA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc20 D O ALA 10 D ALA 10 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc21 D O GLN 293 D GLN 293 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc22 D O ASN 296 D ASN 296 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc23 D OD2 ASP 301 D ASP 301 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc24 D OD1 ASP 304 D ASP 304 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc25 D OD2 ASP 304 D ASP 304 1_555 HA CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc26 E O GLN 293 E GLN 293 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc27 E O ASN 296 E ASN 296 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc28 E OD2 ASP 301 E ASP 301 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc29 E OD1 ASP 304 E ASP 304 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc30 E OD2 ASP 304 E ASP 304 1_555 RA CA CA . E CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? # _chem_comp.formula 'C36 H72 N O8 P' _chem_comp.formula_weight 677.933 _chem_comp.id MC3 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE _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 C1 C2 MC3 sing 216 n n C1 O3P MC3 sing 217 n n C1 H11 MC3 sing 218 n n C1 H12 MC3 sing 219 n n C2 C3 MC3 sing 220 n n C2 O2 MC3 sing 221 n n C2 H2 MC3 sing 222 n n C3 O3 MC3 sing 223 n n C3 H31 MC3 sing 224 n n C3 H32 MC3 sing 225 n n C4 C5 MC3 sing 226 n n C4 O4P MC3 sing 227 n n C4 H41 MC3 sing 228 n n C4 H42 MC3 sing 229 n n C5 N MC3 sing 230 n n C5 H51 MC3 sing 231 n n C5 H52 MC3 sing 232 n n C6 N MC3 sing 233 n n C6 H61 MC3 sing 234 n n C6 H62 MC3 sing 235 n n C6 H63 MC3 sing 236 n n C7 N MC3 sing 237 n n C7 H71 MC3 sing 238 n n C7 H72 MC3 sing 239 n n C7 H73 MC3 sing 240 n n C8 N MC3 sing 241 n n C8 H81 MC3 sing 242 n n C8 H82 MC3 sing 243 n n C8 H83 MC3 sing 244 n n C11 C12 MC3 sing 245 n n C11 O3 MC3 sing 246 n n C11 O11 MC3 doub 247 n n C12 C13 MC3 sing 248 n n C12 H121 MC3 sing 249 n n C12 H122 MC3 sing 250 n n C13 C14 MC3 sing 251 n n C13 H131 MC3 sing 252 n n C13 H132 MC3 sing 253 n n C14 C15 MC3 sing 254 n n C14 H141 MC3 sing 255 n n C14 H142 MC3 sing 256 n n C15 C16 MC3 sing 257 n n C15 H151 MC3 sing 258 n n C15 H152 MC3 sing 259 n n C16 C17 MC3 sing 260 n n C16 H161 MC3 sing 261 n n C16 H162 MC3 sing 262 n n C17 C18 MC3 sing 263 n n C17 H171 MC3 sing 264 n n C17 H172 MC3 sing 265 n n C18 C19 MC3 sing 266 n n C18 H181 MC3 sing 267 n n C18 H182 MC3 sing 268 n n C19 C20 MC3 sing 269 n n C19 H191 MC3 sing 270 n n C19 H192 MC3 sing 271 n n C20 C21 MC3 sing 272 n n C20 H201 MC3 sing 273 n n C20 H202 MC3 sing 274 n n C21 C22 MC3 sing 275 n n C21 H211 MC3 sing 276 n n C21 H212 MC3 sing 277 n n C22 C23 MC3 sing 278 n n C22 H221 MC3 sing 279 n n C22 H222 MC3 sing 280 n n C23 C24 MC3 sing 281 n n C23 H231 MC3 sing 282 n n C23 H232 MC3 sing 283 n n C24 H241 MC3 sing 284 n n C24 H242 MC3 sing 285 n n C24 H243 MC3 sing 286 n n C31 C32 MC3 sing 287 n n C31 O2 MC3 sing 288 n n C31 O31 MC3 doub 289 n n C32 C33 MC3 sing 290 n n C32 H321 MC3 sing 291 n n C32 H322 MC3 sing 292 n n C33 C34 MC3 sing 293 n n C33 H331 MC3 sing 294 n n C33 H332 MC3 sing 295 n n C34 C35 MC3 sing 296 n n C34 H341 MC3 sing 297 n n C34 H342 MC3 sing 298 n n C35 C36 MC3 sing 299 n n C35 H351 MC3 sing 300 n n C35 H352 MC3 sing 301 n n C36 C37 MC3 sing 302 n n C36 H361 MC3 sing 303 n n C36 H362 MC3 sing 304 n n C37 C38 MC3 sing 305 n n C37 H371 MC3 sing 306 n n C37 H372 MC3 sing 307 n n C38 C39 MC3 sing 308 n n C38 H381 MC3 sing 309 n n C38 H382 MC3 sing 310 n n C39 C40 MC3 sing 311 n n C39 H391 MC3 sing 312 n n C39 H392 MC3 sing 313 n n C40 C41 MC3 sing 314 n n C40 H401 MC3 sing 315 n n C40 H402 MC3 sing 316 n n C41 C42 MC3 sing 317 n n C41 H411 MC3 sing 318 n n C41 H412 MC3 sing 319 n n C42 C43 MC3 sing 320 n n C42 H421 MC3 sing 321 n n C42 H422 MC3 sing 322 n n C43 C44 MC3 sing 323 n n C43 H431 MC3 sing 324 n n C43 H432 MC3 sing 325 n n C44 H441 MC3 sing 326 n n C44 H442 MC3 sing 327 n n C44 H443 MC3 sing 328 n n O1P P MC3 doub 329 n n O2P P MC3 sing 330 n n O3P P MC3 sing 331 n n O4P P MC3 sing 332 n n # _atom_sites.entry_id 8D1L _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 F 2 CA B 1 601 378 CA CA . G 3 MC3 B 1 602 601 MC3 MC3 . H 3 MC3 B 1 603 602 MC3 MC3 . I 3 MC3 B 1 604 603 MC3 MC3 . J 3 MC3 B 1 605 604 MC3 MC3 . K 3 MC3 B 1 606 605 MC3 MC3 . L 3 MC3 B 1 607 606 MC3 MC3 . M 3 MC3 B 1 608 607 MC3 MC3 . N 3 MC3 B 1 609 600 MC3 MC3 . O 2 CA C 1 601 378 CA CA . P 3 MC3 C 1 602 601 MC3 MC3 . Q 3 MC3 C 1 603 602 MC3 MC3 . R 3 MC3 C 1 604 603 MC3 MC3 . S 3 MC3 C 1 605 604 MC3 MC3 . T 3 MC3 C 1 606 605 MC3 MC3 . U 3 MC3 C 1 607 606 MC3 MC3 . V 3 MC3 C 1 608 607 MC3 MC3 . W 3 MC3 C 1 609 600 MC3 MC3 . X 3 MC3 A 1 601 600 MC3 MC3 . Y 2 CA A 1 602 378 CA CA . Z 3 MC3 A 1 603 601 MC3 MC3 . AA 3 MC3 A 1 604 602 MC3 MC3 . BA 3 MC3 A 1 605 603 MC3 MC3 . CA 3 MC3 A 1 606 604 MC3 MC3 . DA 3 MC3 A 1 607 605 MC3 MC3 . EA 3 MC3 A 1 608 606 MC3 MC3 . FA 3 MC3 A 1 609 607 MC3 MC3 . GA 4 CL A 1 610 1 CL CL . HA 2 CA D 1 601 378 CA CA . IA 3 MC3 D 1 602 601 MC3 MC3 . JA 3 MC3 D 1 603 602 MC3 MC3 . KA 3 MC3 D 1 604 603 MC3 MC3 . LA 3 MC3 D 1 605 604 MC3 MC3 . MA 3 MC3 D 1 606 605 MC3 MC3 . NA 3 MC3 D 1 607 606 MC3 MC3 . OA 3 MC3 D 1 608 607 MC3 MC3 . PA 3 MC3 D 1 609 600 MC3 MC3 . QA 3 MC3 E 1 601 600 MC3 MC3 . RA 2 CA E 1 602 378 CA CA . SA 3 MC3 E 1 603 601 MC3 MC3 . TA 3 MC3 E 1 604 602 MC3 MC3 . UA 3 MC3 E 1 605 603 MC3 MC3 . VA 3 MC3 E 1 606 604 MC3 MC3 . WA 3 MC3 E 1 607 605 MC3 MC3 . XA 3 MC3 E 1 608 606 MC3 MC3 . YA 3 MC3 E 1 609 607 MC3 MC3 . # 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 C C31 MC3 . . . M 3 196.849 174.037 173.775 1 59.07 ? C31 MC3 608 B 1 HETATM 2 C C32 MC3 . . . M 3 197.182 175.422 173.223 1 59.07 ? C32 MC3 608 B 1 HETATM 3 C C33 MC3 . . . M 3 198.679 175.679 173.368 1 59.07 ? C33 MC3 608 B 1 HETATM 4 C C34 MC3 . . . M 3 199.007 176.163 174.781 1 59.07 ? C34 MC3 608 B 1 HETATM 5 C C35 MC3 . . . M 3 200.02 175.23 175.442 1 59.07 ? C35 MC3 608 B 1 HETATM 6 C C36 MC3 . . . M 3 199.306 174.005 176.015 1 59.07 ? C36 MC3 608 B 1 HETATM 7 C C37 MC3 . . . M 3 200.175 173.351 177.085 1 59.07 ? C37 MC3 608 B 1 HETATM 8 C C38 MC3 . . . M 3 200.06 174.125 178.395 1 59.07 ? C38 MC3 608 B 1 HETATM 9 C C39 MC3 . . . M 3 199.063 173.426 179.315 1 59.07 ? C39 MC3 608 B 1 HETATM 10 C C40 MC3 . . . M 3 198.942 174.193 180.629 1 59.07 ? C40 MC3 608 B 1 HETATM 11 C C41 MC3 . . . M 3 200.241 174.068 181.418 1 59.07 ? C41 MC3 608 B 1 HETATM 12 C C42 MC3 . . . M 3 199.932 173.799 182.887 1 59.07 ? C42 MC3 608 B 1 HETATM 13 C C43 MC3 . . . M 3 199.288 175.03 183.519 1 59.07 ? C43 MC3 608 B 1 HETATM 14 C C44 MC3 . . . M 3 199.205 174.83 185.03 1 59.07 ? C44 MC3 608 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #