data_3C9L # _model_server_result.job_id gU-kgjifRTwT-gu5NFrpjA _model_server_result.datetime_utc '2024-11-23 08:40:15' _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 3c9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1341}' # _entry.id 3C9L # _exptl.entry_id 3C9L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 691.959 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 3C9L _cell.length_a 103.82 _cell.length_b 103.82 _cell.length_c 76.59 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 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 7 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 1335 NAG 2 n B NAG 2 B 2 NAG A 1336 NAG 2 n B BMA 3 B 3 BMA A 1337 BMA 2 n C NAG 1 C 1 NAG A 1338 NAG 2 n C NAG 2 C 2 NAG A 1339 NAG 2 n C BMA 3 C 3 BMA A 1340 BMA # 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 A SG CYS 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 E C ACE . A ACE 0 1_555 A N MET 1 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A ND2 ASN 2 A ASN 2 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 15 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A NZ LYS 296 A LYS 296 1_555 F C15 RET . A RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A SG CYS 322 A CYS 322 1_555 G C1 PLM . A PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? covale ? covale6 A SG CYS 323 A CYS 323 1_555 H C1 PLM . A PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C37 H74 N O8 P' _chem_comp.formula_weight 691.959 _chem_comp.id PEF _chem_comp.mon_nstd_flag . _chem_comp.name DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL # 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 C2 C1 PEF sing 397 n n C2 C3 PEF sing 398 n n C2 O2 PEF sing 399 n n C2 H21 PEF sing 400 n n C1 O3P PEF sing 401 n n C1 H11 PEF sing 402 n n C1 H12 PEF sing 403 n n N C5 PEF sing 404 n n N HN1 PEF sing 405 n n N HN2 PEF sing 406 n n C3 O3 PEF sing 407 n n C3 H31 PEF sing 408 n n C3 H32 PEF sing 409 n n C4 C5 PEF sing 410 n n C4 O4P PEF sing 411 n n C4 H41 PEF sing 412 n n C4 H42 PEF sing 413 n n C5 H51 PEF sing 414 n n C5 H52 PEF sing 415 n n C10 C11 PEF sing 416 n n C10 O4 PEF doub 417 n n C10 O2 PEF sing 418 n n C11 C12 PEF sing 419 n n C11 H112 PEF sing 420 n n C11 H111 PEF sing 421 n n C12 C13 PEF sing 422 n n C12 H122 PEF sing 423 n n C12 H121 PEF sing 424 n n C13 C14 PEF sing 425 n n C13 H132 PEF sing 426 n n C13 H131 PEF sing 427 n n C14 C15 PEF sing 428 n n C14 H142 PEF sing 429 n n C14 H141 PEF sing 430 n n C15 C16 PEF sing 431 n n C15 H152 PEF sing 432 n n C15 H151 PEF sing 433 n n C16 C17 PEF sing 434 n n C16 H162 PEF sing 435 n n C16 H161 PEF sing 436 n n C17 C18 PEF sing 437 n n C17 H172 PEF sing 438 n n C17 H171 PEF sing 439 n n C18 C19 PEF sing 440 n n C18 H182 PEF sing 441 n n C18 H181 PEF sing 442 n n C19 C20 PEF sing 443 n n C19 H192 PEF sing 444 n n C19 H191 PEF sing 445 n n C20 C21 PEF sing 446 n n C20 H202 PEF sing 447 n n C20 H201 PEF sing 448 n n C21 C22 PEF sing 449 n n C21 H212 PEF sing 450 n n C21 H211 PEF sing 451 n n C22 C23 PEF sing 452 n n C22 H222 PEF sing 453 n n C22 H221 PEF sing 454 n n C23 C24 PEF sing 455 n n C23 H232 PEF sing 456 n n C23 H231 PEF sing 457 n n C24 C25 PEF sing 458 n n C24 H242 PEF sing 459 n n C24 H241 PEF sing 460 n n C25 H252 PEF sing 461 n n C25 H251 PEF sing 462 n n C25 H253 PEF sing 463 n n C30 C31 PEF sing 464 n n C30 O5 PEF doub 465 n n C30 O3 PEF sing 466 n n C31 C32 PEF sing 467 n n C31 H312 PEF sing 468 n n C31 H311 PEF sing 469 n n C32 C33 PEF sing 470 n n C32 H322 PEF sing 471 n n C32 H321 PEF sing 472 n n C33 C34 PEF sing 473 n n C33 H332 PEF sing 474 n n C33 H331 PEF sing 475 n n C34 C35 PEF sing 476 n n C34 H342 PEF sing 477 n n C34 H341 PEF sing 478 n n C35 C36 PEF sing 479 n n C35 H352 PEF sing 480 n n C35 H351 PEF sing 481 n n C36 C37 PEF sing 482 n n C36 H362 PEF sing 483 n n C36 H361 PEF sing 484 n n C37 C38 PEF sing 485 n n C37 H372 PEF sing 486 n n C37 H371 PEF sing 487 n n C38 C39 PEF sing 488 n n C38 H382 PEF sing 489 n n C38 H381 PEF sing 490 n n C39 C40 PEF sing 491 n n C39 H392 PEF sing 492 n n C39 H391 PEF sing 493 n n C40 C41 PEF sing 494 n n C40 H402 PEF sing 495 n n C40 H401 PEF sing 496 n n C41 C42 PEF sing 497 n n C41 H412 PEF sing 498 n n C41 H411 PEF sing 499 n n C42 C43 PEF sing 500 n n C42 H422 PEF sing 501 n n C42 H421 PEF sing 502 n n C43 C44 PEF sing 503 n n C43 H432 PEF sing 504 n n C43 H431 PEF sing 505 n n C44 C45 PEF sing 506 n n C44 H442 PEF sing 507 n n C44 H441 PEF sing 508 n n C45 H452 PEF sing 509 n n C45 H451 PEF sing 510 n n C45 H453 PEF sing 511 n n O1P P PEF doub 512 n n O2P P PEF sing 513 n n O2P HOP2 PEF sing 514 n n O3P P PEF sing 515 n n O4P P PEF sing 516 n n # _atom_sites.entry_id 3C9L _atom_sites.fract_transf_matrix[1][1] 0.009632 _atom_sites.fract_transf_matrix[1][2] 0.005561 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011122 _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] 0.013057 _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 D 3 ZN A 1 1349 1349 ZN ZN . E 4 ACE A 1 0 0 ACE ACE . F 5 RET A 1 1332 1332 RET RET . G 6 PLM A 1 1333 1333 PLM PLM . H 6 PLM A 1 1334 1334 PLM PLM . I 7 PEF A 1 1341 1341 PEF PEF . J 8 LDA A 1 1342 1342 LDA LDA . K 9 C8E A 1 1343 1343 C8E C8E . L 9 C8E A 1 1344 1344 C8E C8E . M 9 C8E A 1 1345 1345 C8E C8E . N 9 C8E A 1 1346 1346 C8E C8E . O 9 C8E A 1 1347 1347 C8E C8E . P 9 C8E A 1 1348 1348 C8E C8E . Q 10 HOH A 1 1350 14 HOH HOH . Q 10 HOH A 2 1351 15 HOH HOH . Q 10 HOH A 3 1352 1 HOH HOH . Q 10 HOH A 4 1353 2 HOH HOH . Q 10 HOH A 5 1354 3 HOH HOH . Q 10 HOH A 6 1355 4 HOH HOH . Q 10 HOH A 7 1356 5 HOH HOH . Q 10 HOH A 8 1357 6 HOH HOH . Q 10 HOH A 9 1358 7 HOH HOH . Q 10 HOH A 10 1359 8 HOH HOH . Q 10 HOH A 11 1360 9 HOH HOH . Q 10 HOH A 12 1361 10 HOH HOH . Q 10 HOH A 13 1362 11 HOH HOH . Q 10 HOH A 14 1363 14 HOH HOH . Q 10 HOH A 15 1364 15 HOH HOH . Q 10 HOH A 16 1365 16 HOH HOH . Q 10 HOH A 17 1366 17 HOH HOH . Q 10 HOH A 18 1367 18 HOH HOH . Q 10 HOH A 19 1368 19 HOH HOH . Q 10 HOH A 20 1369 20 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 C10 PEF . . . I 7 -10.119 37.897 8.342 1 68.26 ? C10 PEF 1341 A 1 HETATM 2 C C11 PEF . . . I 7 -9.32 38.992 9.01 1 65.63 ? C11 PEF 1341 A 1 HETATM 3 C C12 PEF . . . I 7 -9.484 40.304 8.243 1 61.6 ? C12 PEF 1341 A 1 HETATM 4 C C13 PEF . . . I 7 -8.15 41.028 8.063 1 64.51 ? C13 PEF 1341 A 1 HETATM 5 C C14 PEF . . . I 7 -8.053 42.305 8.898 1 65.61 ? C14 PEF 1341 A 1 HETATM 6 C C15 PEF . . . I 7 -8.656 43.515 8.177 1 62.42 ? C15 PEF 1341 A 1 HETATM 7 C C16 PEF . . . I 7 -7.997 44.829 8.595 1 59.31 ? C16 PEF 1341 A 1 HETATM 8 C C17 PEF . . . I 7 -8.682 46.014 7.922 1 54.63 ? C17 PEF 1341 A 1 HETATM 9 C C18 PEF . . . I 7 -8.528 47.271 8.77 1 50.57 ? C18 PEF 1341 A 1 HETATM 10 C C30 PEF . . . I 7 -5.671 34.134 7.92 1 95.28 ? C30 PEF 1341 A 1 HETATM 11 C C31 PEF . . . I 7 -5.211 35.252 8.832 1 94.85 ? C31 PEF 1341 A 1 HETATM 12 C C32 PEF . . . I 7 -4.151 36.108 8.141 1 86.95 ? C32 PEF 1341 A 1 HETATM 13 C C33 PEF . . . I 7 -3.987 37.422 8.897 1 91.55 ? C33 PEF 1341 A 1 HETATM 14 C C34 PEF . . . I 7 -3.553 38.581 8.003 1 75.66 ? C34 PEF 1341 A 1 HETATM 15 C C35 PEF . . . I 7 -4.362 39.848 8.291 1 76.09 ? C35 PEF 1341 A 1 HETATM 16 C C36 PEF . . . I 7 -3.47 41.04 8.644 1 68.16 ? C36 PEF 1341 A 1 HETATM 17 C C37 PEF . . . I 7 -4.187 42.379 8.446 1 71.19 ? C37 PEF 1341 A 1 HETATM 18 C C38 PEF . . . I 7 -3.848 43.456 9.486 1 60.86 ? C38 PEF 1341 A 1 HETATM 19 C C39 PEF . . . I 7 -3.642 44.831 8.846 1 57.64 ? C39 PEF 1341 A 1 HETATM 20 C C40 PEF . . . I 7 -4.375 45.969 9.553 1 45.31 ? C40 PEF 1341 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #