data_7WE4 # _model_server_result.job_id iGIH7NRsHjXyEE9pvTBqkg _model_server_result.datetime_utc '2024-11-21 14:04:54' _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 7we4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":2022}' # _entry.id 7WE4 # _exptl.entry_id 7WE4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 792.075 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _entity.pdbx_number_of_molecules 3 _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 7WE4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WE4 _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 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,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? 8 Y N N ? 8 Z N N ? 8 AA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 1803 NAG 2 n B NAG 2 B 2 NAG A 1804 NAG 2 n C NAG 1 C 1 NAG A 1806 NAG 2 n C NAG 2 C 2 NAG A 1807 NAG # 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 276 A CYS 276 1_555 A SG CYS 319 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 310 A CYS 310 1_555 A SG CYS 325 A CYS 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 857 A CYS 857 1_555 A SG CYS 866 A CYS 866 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 1310 A CYS 1310 1_555 A SG CYS 1332 A CYS 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 A SG CYS 1678 A CYS 1678 1_555 A SG CYS 1692 A CYS 1692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? covale ? covale1 A ND2 ASN 312 A ASN 312 1_555 E C1 NAG . A NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.531 ? covale ? covale2 A ND2 ASN 819 A ASN 819 1_555 D C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 A ND2 ASN 1312 A ASN 1312 1_555 F C1 NAG . A NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 A ND2 ASN 1328 A ASN 1328 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.585 ? covale ? covale5 A ND2 ASN 1336 A ASN 1336 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C42 H82 N O10 P' _chem_comp.formula_weight 792.075 _chem_comp.id P5S _chem_comp.mon_nstd_flag . _chem_comp.name O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'phosphatidyl serine' # 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 CA C P5S sing 475 n n O C P5S doub 476 n n C OXT P5S sing 477 n n CA N P5S sing 478 n n N HN P5S sing 479 n n N HNA P5S sing 480 n n O19 C1 P5S sing 481 n n C1 C2 P5S sing 482 n n C1 H1 P5S sing 483 n n C1 H1A P5S sing 484 n n C2 O37 P5S sing 485 n n C2 C3 P5S sing 486 n n C2 H2 P5S sing 487 n n O16 C3 P5S sing 488 n n C3 H3 P5S sing 489 n n C3 H3A P5S sing 490 n n CB CA P5S sing 491 n n CA HA P5S sing 492 n n CB OG P5S sing 493 n n CB HB P5S sing 494 n n CB HBA P5S sing 495 n n P12 OG P5S sing 496 n n O16 P12 P5S sing 497 n n O13 P12 P5S doub 498 n n P12 O15 P5S sing 499 n n O15 HO15 P5S sing 500 n n C20 C17 P5S sing 501 n n O19 C17 P5S sing 502 n n C17 O18 P5S doub 503 n n C21 C20 P5S sing 504 n n C20 H20 P5S sing 505 n n C20 H20A P5S sing 506 n n C21 C22 P5S sing 507 n n C21 H21 P5S sing 508 n n C21 H21A P5S sing 509 n n C23 C22 P5S sing 510 n n C22 H22 P5S sing 511 n n C22 H22A P5S sing 512 n n C24 C23 P5S sing 513 n n C23 H23 P5S sing 514 n n C23 H23A P5S sing 515 n n C25 C24 P5S sing 516 n n C24 H24 P5S sing 517 n n C24 H24A P5S sing 518 n n C26 C25 P5S sing 519 n n C25 H25 P5S sing 520 n n C25 H25A P5S sing 521 n n C26 C27 P5S sing 522 n n C26 H26 P5S sing 523 n n C26 H26A P5S sing 524 n n C27 C28 P5S sing 525 n n C27 H27 P5S sing 526 n n C27 H27A P5S sing 527 n n C29 C28 P5S sing 528 n n C28 H28 P5S sing 529 n n C28 H28A P5S sing 530 n n C30 C29 P5S sing 531 n n C29 H29 P5S sing 532 n n C29 H29A P5S sing 533 n n C31 C30 P5S sing 534 n n C30 H30 P5S sing 535 n n C30 H30A P5S sing 536 n n C31 C32 P5S sing 537 n n C31 H31 P5S sing 538 n n C31 H31A P5S sing 539 n n C33 C32 P5S sing 540 n n C32 H32 P5S sing 541 n n C32 H32A P5S sing 542 n n C33 C34 P5S sing 543 n n C33 H33 P5S sing 544 n n C33 H33A P5S sing 545 n n C35 C34 P5S sing 546 n n C34 H34 P5S sing 547 n n C34 H34A P5S sing 548 n n C36 C35 P5S sing 549 n n C35 H35 P5S sing 550 n n C35 H35A P5S sing 551 n n C36 H36 P5S sing 552 n n C36 H36A P5S sing 553 n n C36 H36B P5S sing 554 n n C38 O37 P5S sing 555 n n O47 C38 P5S doub 556 n n C38 C39 P5S sing 557 n n C40 C39 P5S sing 558 n n C39 H39 P5S sing 559 n n C39 H39A P5S sing 560 n n C41 C40 P5S sing 561 n n C40 H40 P5S sing 562 n n C40 H40A P5S sing 563 n n C42 C41 P5S sing 564 n n C41 H41 P5S sing 565 n n C41 H41A P5S sing 566 n n C43 C42 P5S sing 567 n n C42 H42 P5S sing 568 n n C42 H42A P5S sing 569 n n C43 C44 P5S sing 570 n n C43 H43 P5S sing 571 n n C43 H43A P5S sing 572 n n C44 C45 P5S sing 573 n n C44 H44 P5S sing 574 n n C44 H44A P5S sing 575 n n C45 C46 P5S sing 576 n n C45 H45 P5S sing 577 n n C45 H45A P5S sing 578 n n C46 C48 P5S sing 579 n n C46 H46 P5S sing 580 n n C46 H46A P5S sing 581 n n C48 C49 P5S sing 582 n n C48 H48 P5S sing 583 n n C48 H48A P5S sing 584 n n C49 C50 P5S sing 585 n n C49 H49 P5S sing 586 n n C49 H49A P5S sing 587 n n C50 C51 P5S sing 588 n n C50 H50 P5S sing 589 n n C50 H50A P5S sing 590 n n C51 C52 P5S sing 591 n n C51 H51 P5S sing 592 n n C51 H51A P5S sing 593 n n C53 C52 P5S sing 594 n n C52 H52 P5S sing 595 n n C52 H52A P5S sing 596 n n C53 C54 P5S sing 597 n n C53 H53 P5S sing 598 n n C53 H53A P5S sing 599 n n C55 C54 P5S sing 600 n n C54 H54 P5S sing 601 n n C54 H54A P5S sing 602 n n C55 C56 P5S sing 603 n n C55 H55 P5S sing 604 n n C55 H55A P5S sing 605 n n C56 H56 P5S sing 606 n n C56 H56A P5S sing 607 n n C56 H56B P5S sing 608 n n OXT HXT P5S sing 609 n n # _atom_sites.entry_id 7WE4 _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 D 3 NAG A 1 2001 1801 NAG NAG . E 3 NAG A 1 2002 1802 NAG NAG . F 3 NAG A 1 2003 1805 NAG NAG . G 4 95T A 1 2004 1901 95T LIG . H 5 CLR A 1 2005 2001 CLR CLR . I 6 PCW A 1 2006 2003 PCW PCW . J 6 PCW A 1 2007 2004 PCW PCW . K 7 LPE A 1 2008 2005 LPE LPE . L 7 LPE A 1 2009 2006 LPE LPE . M 6 PCW A 1 2010 2007 PCW PCW . N 7 LPE A 1 2011 2008 LPE LPE . O 7 LPE A 1 2012 2009 LPE LPE . P 6 PCW A 1 2013 2010 PCW PCW . Q 6 PCW A 1 2014 2014 PCW PCW . R 7 LPE A 1 2015 2016 LPE LPE . S 5 CLR A 1 2016 2017 CLR CLR . T 7 LPE A 1 2017 2018 LPE LPE . U 7 LPE A 1 2018 2019 LPE LPE . V 7 LPE A 1 2019 2020 LPE LPE . W 7 LPE A 1 2020 2021 LPE LPE . X 5 CLR A 1 2021 2022 CLR CLR . Y 8 P5S A 1 2022 2101 P5S P5S . Z 8 P5S A 1 2023 2102 P5S P5S . AA 8 P5S A 1 2024 2103 P5S P5S . BA 5 CLR A 1 2025 1 CLR CLR . # 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 C P5S . . . Y 8 121.377 151.219 149.25 1 20 ? C P5S 2022 A 1 HETATM 2 N N P5S . . . Y 8 121.576 149.023 150.246 1 20 ? N P5S 2022 A 1 HETATM 3 O O P5S . . . Y 8 120.55 152.065 149.547 1 20 ? O P5S 2022 A 1 HETATM 4 C C1 P5S . . . Y 8 123.292 150.111 145.044 1 20 ? C1 P5S 2022 A 1 HETATM 5 C C2 P5S . . . Y 8 124.538 150.878 145.428 1 20 ? C2 P5S 2022 A 1 HETATM 6 C C3 P5S . . . Y 8 124.88 150.569 146.878 1 20 ? C3 P5S 2022 A 1 HETATM 7 C CA P5S . . . Y 8 122.061 150.415 150.314 1 20 ? CA P5S 2022 A 1 HETATM 8 C CB P5S . . . Y 8 123.56 150.403 150.105 1 20 ? CB P5S 2022 A 1 HETATM 9 O OG P5S . . . Y 8 124.076 151.694 149.789 1 20 ? OG P5S 2022 A 1 HETATM 10 P P12 P5S . . . Y 8 125.544 151.798 149.139 1 20 ? P12 P5S 2022 A 1 HETATM 11 O O13 P5S . . . Y 8 126.175 153.086 149.493 1 20 ? O13 P5S 2022 A 1 HETATM 12 O O15 P5S . . . Y 8 126.414 150.562 149.686 1 20 ? O15 P5S 2022 A 1 HETATM 13 O O16 P5S . . . Y 8 125.436 151.706 147.539 1 20 ? O16 P5S 2022 A 1 HETATM 14 C C17 P5S . . . Y 8 123.557 149.297 142.728 1 20 ? C17 P5S 2022 A 1 HETATM 15 O O18 P5S . . . Y 8 124.086 148.311 143.169 1 20 ? O18 P5S 2022 A 1 HETATM 16 O O19 P5S . . . Y 8 123.068 150.283 143.655 1 20 ? O19 P5S 2022 A 1 HETATM 17 C C20 P5S . . . Y 8 123.406 149.459 141.248 1 20 ? C20 P5S 2022 A 1 HETATM 18 C C21 P5S . . . Y 8 124.106 148.292 140.584 1 20 ? C21 P5S 2022 A 1 HETATM 19 C C22 P5S . . . Y 8 123.875 148.325 139.095 1 20 ? C22 P5S 2022 A 1 HETATM 20 C C23 P5S . . . Y 8 124.558 147.151 138.436 1 20 ? C23 P5S 2022 A 1 HETATM 21 C C24 P5S . . . Y 8 124.11 147.125 136.995 1 20 ? C24 P5S 2022 A 1 HETATM 22 C C25 P5S . . . Y 8 124.543 145.864 136.28 1 20 ? C25 P5S 2022 A 1 HETATM 23 C C26 P5S . . . Y 8 123.647 145.658 135.075 1 20 ? C26 P5S 2022 A 1 HETATM 24 C C27 P5S . . . Y 8 124.173 144.535 134.207 1 20 ? C27 P5S 2022 A 1 HETATM 25 C C28 P5S . . . Y 8 123.284 144.305 132.997 1 20 ? C28 P5S 2022 A 1 HETATM 26 C C29 P5S . . . Y 8 123.788 143.128 132.177 1 20 ? C29 P5S 2022 A 1 HETATM 27 C C30 P5S . . . Y 8 122.855 142.828 131.015 1 20 ? C30 P5S 2022 A 1 HETATM 28 C C31 P5S . . . Y 8 121.396 142.842 131.445 1 20 ? C31 P5S 2022 A 1 HETATM 29 O O37 P5S . . . Y 8 124.213 152.243 145.285 1 20 ? O37 P5S 2022 A 1 HETATM 30 C C38 P5S . . . Y 8 125.283 153.004 144.691 1 20 ? C38 P5S 2022 A 1 HETATM 31 C C39 P5S . . . Y 8 125.696 152.74 143.272 1 20 ? C39 P5S 2022 A 1 HETATM 32 C C40 P5S . . . Y 8 125.048 153.82 142.431 1 20 ? C40 P5S 2022 A 1 HETATM 33 C C41 P5S . . . Y 8 125.6 153.845 141.026 1 20 ? C41 P5S 2022 A 1 HETATM 34 C C42 P5S . . . Y 8 125.517 152.485 140.374 1 20 ? C42 P5S 2022 A 1 HETATM 35 C C43 P5S . . . Y 8 125.547 152.696 138.875 1 20 ? C43 P5S 2022 A 1 HETATM 36 C C44 P5S . . . Y 8 125.8 151.392 138.154 1 20 ? C44 P5S 2022 A 1 HETATM 37 C C45 P5S . . . Y 8 126.08 151.641 136.686 1 20 ? C45 P5S 2022 A 1 HETATM 38 C C46 P5S . . . Y 8 126.571 150.358 136.052 1 20 ? C46 P5S 2022 A 1 HETATM 39 O O47 P5S . . . Y 8 125.796 153.883 145.349 1 20 ? O47 P5S 2022 A 1 HETATM 40 C C48 P5S . . . Y 8 126.682 150.53 134.554 1 20 ? C48 P5S 2022 A 1 HETATM 41 C C49 P5S . . . Y 8 126.47 149.181 133.892 1 20 ? C49 P5S 2022 A 1 HETATM 42 C C50 P5S . . . Y 8 126.423 149.293 132.376 1 20 ? C50 P5S 2022 A 1 HETATM 43 C C51 P5S . . . Y 8 127.805 149.598 131.825 1 20 ? C51 P5S 2022 A 1 HETATM 44 C C52 P5S . . . Y 8 127.82 149.542 130.305 1 20 ? C52 P5S 2022 A 1 HETATM 45 O OXT P5S . . . Y 8 121.646 151.028 147.962 1 20 ? OXT P5S 2022 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #