data_3DDL # _model_server_result.job_id uPWY7zclfuf7qmzEh_fG-g _model_server_result.datetime_utc '2024-11-27 03:58:07' _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 3ddl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":1416}' # _entry.id 3DDL # _exptl.entry_id 3DDL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 787.121 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 76.35 _cell.angle_beta 74.93 _cell.angle_gamma 64.08 _cell.entry_id 3DDL _cell.length_a 52.74 _cell.length_b 59.49 _cell.length_c 59.72 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,DA 1 1 B,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,EA 2 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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id CA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A NZ LYS 240 A LYS 240 1_555 L C15 RET . A RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 B NZ LYS 240 B LYS 240 1_555 AA C15 RET . B RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C44 H85 N O8 P 1' _chem_comp.formula_weight 787.121 _chem_comp.id PCW _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE # 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 PCW sing 224 n n C1 O3P PCW sing 225 n n C1 H11 PCW sing 226 n n C1 H12 PCW sing 227 n n C2 C3 PCW sing 228 n n C2 O2 PCW sing 229 n n C2 H2 PCW sing 230 n n C3 O3 PCW sing 231 n n C3 H31 PCW sing 232 n n C3 H32 PCW sing 233 n n C4 C5 PCW sing 234 n n C4 O4P PCW sing 235 n n C4 H41 PCW sing 236 n n C4 H42 PCW sing 237 n n C5 N PCW sing 238 n n C5 H51 PCW sing 239 n n C5 H52 PCW sing 240 n n C6 N PCW sing 241 n n C6 H61 PCW sing 242 n n C6 H62 PCW sing 243 n n C6 H63 PCW sing 244 n n C7 N PCW sing 245 n n C7 H71 PCW sing 246 n n C7 H72 PCW sing 247 n n C7 H73 PCW sing 248 n n C8 N PCW sing 249 n n C8 H81 PCW sing 250 n n C8 H82 PCW sing 251 n n C8 H83 PCW sing 252 n n C11 C12 PCW sing 253 n n C11 O3 PCW sing 254 n n C11 O11 PCW doub 255 n n C12 C13 PCW sing 256 n n C12 H121 PCW sing 257 n n C12 H122 PCW sing 258 n n C13 C14 PCW sing 259 n n C13 H131 PCW sing 260 n n C13 H132 PCW sing 261 n n C14 C15 PCW sing 262 n n C14 H141 PCW sing 263 n n C14 H142 PCW sing 264 n n C15 C16 PCW sing 265 n n C15 H151 PCW sing 266 n n C15 H152 PCW sing 267 n n C16 C17 PCW sing 268 n n C16 H161 PCW sing 269 n n C16 H162 PCW sing 270 n n C17 C18 PCW sing 271 n n C17 H171 PCW sing 272 n n C17 H172 PCW sing 273 n n C18 C19 PCW sing 274 n n C18 H181 PCW sing 275 n n C18 H182 PCW sing 276 n n C19 C20 PCW doub 277 z n C19 H19 PCW sing 278 n n C20 C21 PCW sing 279 n n C20 H20 PCW sing 280 n n C21 C22 PCW sing 281 n n C21 H211 PCW sing 282 n n C21 H212 PCW sing 283 n n C22 C23 PCW sing 284 n n C22 H221 PCW sing 285 n n C22 H222 PCW sing 286 n n C23 C24 PCW sing 287 n n C23 H231 PCW sing 288 n n C23 H232 PCW sing 289 n n C24 C25 PCW sing 290 n n C24 H241 PCW sing 291 n n C24 H242 PCW sing 292 n n C25 C26 PCW sing 293 n n C25 H251 PCW sing 294 n n C25 H252 PCW sing 295 n n C26 C27 PCW sing 296 n n C26 H261 PCW sing 297 n n C26 H262 PCW sing 298 n n C27 C28 PCW sing 299 n n C27 H271 PCW sing 300 n n C27 H272 PCW sing 301 n n C28 H281 PCW sing 302 n n C28 H282 PCW sing 303 n n C28 H283 PCW sing 304 n n C31 C32 PCW sing 305 n n C31 O2 PCW sing 306 n n C31 O31 PCW doub 307 n n C32 C33 PCW sing 308 n n C32 H321 PCW sing 309 n n C32 H322 PCW sing 310 n n C33 C34 PCW sing 311 n n C33 H331 PCW sing 312 n n C33 H332 PCW sing 313 n n C34 C35 PCW sing 314 n n C34 H341 PCW sing 315 n n C34 H342 PCW sing 316 n n C35 C36 PCW sing 317 n n C35 H351 PCW sing 318 n n C35 H352 PCW sing 319 n n C36 C37 PCW sing 320 n n C36 H361 PCW sing 321 n n C36 H362 PCW sing 322 n n C37 C38 PCW sing 323 n n C37 H371 PCW sing 324 n n C37 H372 PCW sing 325 n n C38 C39 PCW sing 326 n n C38 H381 PCW sing 327 n n C38 H382 PCW sing 328 n n C39 C40 PCW doub 329 z n C39 H39 PCW sing 330 n n C40 C41 PCW sing 331 n n C40 H40 PCW sing 332 n n C41 C42 PCW sing 333 n n C41 H411 PCW sing 334 n n C41 H412 PCW sing 335 n n C42 C43 PCW sing 336 n n C42 H421 PCW sing 337 n n C42 H422 PCW sing 338 n n C43 C44 PCW sing 339 n n C43 H431 PCW sing 340 n n C43 H432 PCW sing 341 n n C44 C45 PCW sing 342 n n C44 H441 PCW sing 343 n n C44 H442 PCW sing 344 n n C45 C46 PCW sing 345 n n C45 H451 PCW sing 346 n n C45 H452 PCW sing 347 n n C46 C47 PCW sing 348 n n C46 H461 PCW sing 349 n n C46 H462 PCW sing 350 n n C47 C48 PCW sing 351 n n C47 H471 PCW sing 352 n n C47 H472 PCW sing 353 n n C48 H481 PCW sing 354 n n C48 H482 PCW sing 355 n n C48 H483 PCW sing 356 n n O1P P PCW sing 357 n n O1P H1P PCW sing 358 n n O2P P PCW doub 359 n n O3P P PCW sing 360 n n O4P P PCW sing 361 n n # _atom_sites.entry_id 3DDL _atom_sites.fract_transf_matrix[1][1] 0.018961 _atom_sites.fract_transf_matrix[1][2] -0.009215 _atom_sites.fract_transf_matrix[1][3] -0.003846 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01869 _atom_sites.fract_transf_matrix[2][3] -0.002659 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017516 _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 C 2 SXN A 1 1401 1401 SXN SXN . D 3 UNL A 1 1402 1402 UNL UNL . E 3 UNL A 1 1403 1403 UNL UNL . F 3 UNL A 1 1404 1404 UNL UNL . G 3 UNL A 1 1405 1405 UNL UNL . H 3 UNL A 1 1406 1406 UNL UNL . I 3 UNL A 1 1407 1407 UNL UNL . J 3 UNL A 1 1408 1408 UNL UNL . K 3 UNL A 1 1409 1409 UNL UNL . L 4 RET A 1 1301 1301 RET RET . M 2 SXN B 1 1401 1401 SXN SXN . N 3 UNL B 1 1402 1402 UNL UNL . O 3 UNL B 1 1403 1403 UNL UNL . P 3 UNL B 1 1404 1404 UNL UNL . Q 3 UNL B 1 1405 1405 UNL UNL . R 3 UNL B 1 1406 1406 UNL UNL . S 3 UNL B 1 1407 1407 UNL UNL . T 3 UNL B 1 1408 1408 UNL UNL . U 3 UNL B 1 1409 1409 UNL UNL . V 3 UNL B 1 1410 1410 UNL UNL . W 3 UNL B 1 1411 1411 UNL UNL . X 3 UNL B 1 1412 1412 UNL UNL . Y 3 UNL B 1 1413 1413 UNL UNL . Z 3 UNL B 1 1414 1414 UNL UNL . AA 4 RET B 1 1301 1301 RET RET . BA 5 PX4 B 1 1415 1415 PX4 PX4 . CA 6 PCW B 1 1416 1416 PCW PCW . DA 7 HOH A 1 402 402 HOH HOH . DA 7 HOH A 2 413 413 HOH HOH . DA 7 HOH A 3 414 414 HOH HOH . DA 7 HOH A 4 415 415 HOH HOH . DA 7 HOH A 5 416 416 HOH HOH . DA 7 HOH A 6 417 417 HOH HOH . DA 7 HOH A 7 418 418 HOH HOH . DA 7 HOH A 8 419 419 HOH HOH . DA 7 HOH A 9 420 420 HOH HOH . DA 7 HOH A 10 421 421 HOH HOH . DA 7 HOH A 11 422 422 HOH HOH . DA 7 HOH A 12 423 423 HOH HOH . DA 7 HOH A 13 424 424 HOH HOH . DA 7 HOH A 14 425 425 HOH HOH . DA 7 HOH A 15 426 426 HOH HOH . DA 7 HOH A 16 427 427 HOH HOH . DA 7 HOH A 17 428 428 HOH HOH . DA 7 HOH A 18 429 429 HOH HOH . DA 7 HOH A 19 430 430 HOH HOH . DA 7 HOH A 20 431 431 HOH HOH . DA 7 HOH A 21 432 432 HOH HOH . DA 7 HOH A 22 433 433 HOH HOH . DA 7 HOH A 23 434 434 HOH HOH . DA 7 HOH A 24 435 435 HOH HOH . DA 7 HOH A 25 436 436 HOH HOH . DA 7 HOH A 26 437 437 HOH HOH . DA 7 HOH A 27 438 438 HOH HOH . DA 7 HOH A 28 439 439 HOH HOH . DA 7 HOH A 29 440 440 HOH HOH . DA 7 HOH A 30 441 441 HOH HOH . DA 7 HOH A 31 442 442 HOH HOH . DA 7 HOH A 32 443 443 HOH HOH . DA 7 HOH A 33 501 501 HOH HOH . DA 7 HOH A 34 502 502 HOH HOH . EA 7 HOH B 1 402 402 HOH HOH . EA 7 HOH B 2 420 420 HOH HOH . EA 7 HOH B 3 421 421 HOH HOH . EA 7 HOH B 4 422 422 HOH HOH . EA 7 HOH B 5 423 423 HOH HOH . EA 7 HOH B 6 424 424 HOH HOH . EA 7 HOH B 7 425 425 HOH HOH . EA 7 HOH B 8 426 426 HOH HOH . EA 7 HOH B 9 427 427 HOH HOH . EA 7 HOH B 10 428 428 HOH HOH . EA 7 HOH B 11 429 429 HOH HOH . EA 7 HOH B 12 430 430 HOH HOH . EA 7 HOH B 13 431 431 HOH HOH . EA 7 HOH B 14 432 432 HOH HOH . EA 7 HOH B 15 433 433 HOH HOH . EA 7 HOH B 16 434 434 HOH HOH . EA 7 HOH B 17 435 435 HOH HOH . EA 7 HOH B 18 436 436 HOH HOH . EA 7 HOH B 19 437 437 HOH HOH . EA 7 HOH B 20 438 438 HOH HOH . EA 7 HOH B 21 439 439 HOH HOH . EA 7 HOH B 22 440 440 HOH HOH . EA 7 HOH B 23 441 441 HOH HOH . EA 7 HOH B 24 442 442 HOH HOH . EA 7 HOH B 25 443 443 HOH HOH . EA 7 HOH B 26 444 444 HOH HOH . EA 7 HOH B 27 501 501 HOH HOH . EA 7 HOH B 28 502 502 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 C C1 PCW . . . CA 6 44.522 54.324 59.788 1 87.74 ? C1 PCW 1416 B 1 HETATM 2 C C2 PCW . . . CA 6 44.439 52.991 59.035 1 86 ? C2 PCW 1416 B 1 HETATM 3 C C3 PCW . . . CA 6 45.86 52.421 58.857 1 84.99 ? C3 PCW 1416 B 1 HETATM 4 C C11 PCW . . . CA 6 46.761 52.652 56.495 1 81.87 ? C11 PCW 1416 B 1 HETATM 5 C C12 PCW . . . CA 6 47.479 51.915 55.383 1 80.11 ? C12 PCW 1416 B 1 HETATM 6 C C13 PCW . . . CA 6 46.471 51.497 54.312 1 77.6 ? C13 PCW 1416 B 1 HETATM 7 C C14 PCW . . . CA 6 46.952 51.99 52.948 1 76.32 ? C14 PCW 1416 B 1 HETATM 8 C C15 PCW . . . CA 6 46.315 51.151 51.842 1 74.61 ? C15 PCW 1416 B 1 HETATM 9 C C16 PCW . . . CA 6 46.13 52.018 50.588 1 73.55 ? C16 PCW 1416 B 1 HETATM 10 C C17 PCW . . . CA 6 44.955 51.491 49.764 1 71.88 ? C17 PCW 1416 B 1 HETATM 11 C C18 PCW . . . CA 6 45.208 51.711 48.275 1 70.23 ? C18 PCW 1416 B 1 HETATM 12 C C19 PCW . . . CA 6 45.047 50.386 47.533 1 68.52 ? C19 PCW 1416 B 1 HETATM 13 C C20 PCW . . . CA 6 43.835 50.47 46.599 1 68.24 ? C20 PCW 1416 B 1 HETATM 14 C C21 PCW . . . CA 6 43.024 49.172 46.655 1 65.55 ? C21 PCW 1416 B 1 HETATM 15 C C22 PCW . . . CA 6 42.726 48.725 45.226 1 63.46 ? C22 PCW 1416 B 1 HETATM 16 C C23 PCW . . . CA 6 41.556 47.755 45.211 1 60.74 ? C23 PCW 1416 B 1 HETATM 17 C C24 PCW . . . CA 6 41.184 47.439 43.766 1 59.09 ? C24 PCW 1416 B 1 HETATM 18 C C25 PCW . . . CA 6 39.964 48.259 43.338 1 58.04 ? C25 PCW 1416 B 1 HETATM 19 C C26 PCW . . . CA 6 40.184 48.816 41.931 1 57.17 ? C26 PCW 1416 B 1 HETATM 20 C C27 PCW . . . CA 6 38.846 49.049 41.237 1 58.47 ? C27 PCW 1416 B 1 HETATM 21 C C28 PCW . . . CA 6 39.05 49.052 39.737 1 56.45 ? C28 PCW 1416 B 1 HETATM 22 C C31 PCW . . . CA 6 42.495 52.715 57.376 1 84.68 ? C31 PCW 1416 B 1 HETATM 23 C C32 PCW . . . CA 6 42.015 52.841 55.946 1 83.01 ? C32 PCW 1416 B 1 HETATM 24 C C33 PCW . . . CA 6 42.322 51.549 55.19 1 80.98 ? C33 PCW 1416 B 1 HETATM 25 C C34 PCW . . . CA 6 42.615 51.875 53.731 1 79.85 ? C34 PCW 1416 B 1 HETATM 26 C C35 PCW . . . CA 6 41.829 50.937 52.822 1 78.55 ? C35 PCW 1416 B 1 HETATM 27 C C36 PCW . . . CA 6 41.48 51.667 51.528 1 77.32 ? C36 PCW 1416 B 1 HETATM 28 C C37 PCW . . . CA 6 41.274 50.654 50.408 1 77.68 ? C37 PCW 1416 B 1 HETATM 29 C C38 PCW . . . CA 6 40.535 51.32 49.249 1 76.76 ? C38 PCW 1416 B 1 HETATM 30 C C39 PCW . . . CA 6 39.58 50.318 48.606 1 77.21 ? C39 PCW 1416 B 1 HETATM 31 C C40 PCW . . . CA 6 39.599 50.503 47.092 1 76.9 ? C40 PCW 1416 B 1 HETATM 32 O O2 PCW . . . CA 6 43.836 53.216 57.736 1 85.45 ? O2 PCW 1416 B 1 HETATM 33 O O3 PCW . . . CA 6 46.036 51.897 57.524 1 83.34 ? O3 PCW 1416 B 1 HETATM 34 O O11 PCW . . . CA 6 46.786 53.885 56.529 1 82.57 ? O11 PCW 1416 B 1 HETATM 35 O O31 PCW . . . CA 6 41.766 52.208 58.219 1 85.83 ? O31 PCW 1416 B 1 HETATM 36 O O1P PCW . . . CA 6 44.084 56.429 62.019 1 92.22 ? O1P PCW 1416 B 1 HETATM 37 O O2P PCW . . . CA 6 46.506 55.924 61.754 1 90.99 ? O2P PCW 1416 B 1 HETATM 38 O O3P PCW . . . CA 6 44.807 54.095 61.171 1 90.33 ? O3P PCW 1416 B 1 HETATM 39 O O4P PCW . . . CA 6 45.207 54.866 63.584 1 91.2 ? O4P PCW 1416 B 1 HETATM 40 P P PCW . . . CA 6 45.156 55.347 62.147 1 92.8 ? P PCW 1416 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #