data_7W9M # _model_server_result.job_id ZVXuxMdYrq0aybNwcJPqpQ _model_server_result.datetime_utc '2024-11-22 01:38:17' _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 7w9m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2004}' # _entry.id 7W9M # _exptl.entry_id 7W9M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 792.075 _entity.id 7 _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 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 90 _cell.entry_id 7W9M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W9M _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _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 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 E 1 NAG E 304 NAG 4 n D NAG 2 E 2 NAG E 305 NAG 4 n E NAG 1 D 1 NAG D 2007 NAG 4 n E NAG 2 D 2 NAG D 2008 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 318 A CYS 275 1_555 A SG CYS 367 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 358 A CYS 315 1_555 A SG CYS 373 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 940 A CYS 897 1_555 A SG CYS 946 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 978 A CYS 935 1_555 A SG CYS 987 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 A SG CYS 1393 A CYS 1350 1_555 A SG CYS 1413 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 1758 A CYS 1715 1_555 A SG CYS 1773 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf10 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 326 A ASN 283 1_555 G C1 NAG . A NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 1395 A ASN 1352 1_555 E C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 A ND2 ASN 1409 A ASN 1366 1_555 H C1 NAG . A NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.583 ? covale ? covale4 A ND2 ASN 1418 A ASN 1375 1_555 N C1 NAG . A NAG 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? covale ? covale5 B ND2 ASN 93 B ASN 93 1_555 P C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 Q C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? covale ? covale7 B ND2 ASN 114 B ASN 114 1_555 R C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? covale ? covale8 B ND2 ASN 135 B ASN 135 1_555 D C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 D O4 NAG . E NAG 1 1_555 D C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale10 E O4 NAG . D NAG 1 1_555 E C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 397 n n O C P5S doub 398 n n C OXT P5S sing 399 n n CA N P5S sing 400 n n N HN P5S sing 401 n n N HNA P5S sing 402 n n O19 C1 P5S sing 403 n n C1 C2 P5S sing 404 n n C1 H1 P5S sing 405 n n C1 H1A P5S sing 406 n n C2 O37 P5S sing 407 n n C2 C3 P5S sing 408 n n C2 H2 P5S sing 409 n n O16 C3 P5S sing 410 n n C3 H3 P5S sing 411 n n C3 H3A P5S sing 412 n n CB CA P5S sing 413 n n CA HA P5S sing 414 n n CB OG P5S sing 415 n n CB HB P5S sing 416 n n CB HBA P5S sing 417 n n P12 OG P5S sing 418 n n O16 P12 P5S sing 419 n n O13 P12 P5S doub 420 n n P12 O15 P5S sing 421 n n O15 HO15 P5S sing 422 n n C20 C17 P5S sing 423 n n O19 C17 P5S sing 424 n n C17 O18 P5S doub 425 n n C21 C20 P5S sing 426 n n C20 H20 P5S sing 427 n n C20 H20A P5S sing 428 n n C21 C22 P5S sing 429 n n C21 H21 P5S sing 430 n n C21 H21A P5S sing 431 n n C23 C22 P5S sing 432 n n C22 H22 P5S sing 433 n n C22 H22A P5S sing 434 n n C24 C23 P5S sing 435 n n C23 H23 P5S sing 436 n n C23 H23A P5S sing 437 n n C25 C24 P5S sing 438 n n C24 H24 P5S sing 439 n n C24 H24A P5S sing 440 n n C26 C25 P5S sing 441 n n C25 H25 P5S sing 442 n n C25 H25A P5S sing 443 n n C26 C27 P5S sing 444 n n C26 H26 P5S sing 445 n n C26 H26A P5S sing 446 n n C27 C28 P5S sing 447 n n C27 H27 P5S sing 448 n n C27 H27A P5S sing 449 n n C29 C28 P5S sing 450 n n C28 H28 P5S sing 451 n n C28 H28A P5S sing 452 n n C30 C29 P5S sing 453 n n C29 H29 P5S sing 454 n n C29 H29A P5S sing 455 n n C31 C30 P5S sing 456 n n C30 H30 P5S sing 457 n n C30 H30A P5S sing 458 n n C31 C32 P5S sing 459 n n C31 H31 P5S sing 460 n n C31 H31A P5S sing 461 n n C33 C32 P5S sing 462 n n C32 H32 P5S sing 463 n n C32 H32A P5S sing 464 n n C33 C34 P5S sing 465 n n C33 H33 P5S sing 466 n n C33 H33A P5S sing 467 n n C35 C34 P5S sing 468 n n C34 H34 P5S sing 469 n n C34 H34A P5S sing 470 n n C36 C35 P5S sing 471 n n C35 H35 P5S sing 472 n n C35 H35A P5S sing 473 n n C36 H36 P5S sing 474 n n C36 H36A P5S sing 475 n n C36 H36B P5S sing 476 n n C38 O37 P5S sing 477 n n O47 C38 P5S doub 478 n n C38 C39 P5S sing 479 n n C40 C39 P5S sing 480 n n C39 H39 P5S sing 481 n n C39 H39A P5S sing 482 n n C41 C40 P5S sing 483 n n C40 H40 P5S sing 484 n n C40 H40A P5S sing 485 n n C42 C41 P5S sing 486 n n C41 H41 P5S sing 487 n n C41 H41A P5S sing 488 n n C43 C42 P5S sing 489 n n C42 H42 P5S sing 490 n n C42 H42A P5S sing 491 n n C43 C44 P5S sing 492 n n C43 H43 P5S sing 493 n n C43 H43A P5S sing 494 n n C44 C45 P5S sing 495 n n C44 H44 P5S sing 496 n n C44 H44A P5S sing 497 n n C45 C46 P5S sing 498 n n C45 H45 P5S sing 499 n n C45 H45A P5S sing 500 n n C46 C48 P5S sing 501 n n C46 H46 P5S sing 502 n n C46 H46A P5S sing 503 n n C48 C49 P5S sing 504 n n C48 H48 P5S sing 505 n n C48 H48A P5S sing 506 n n C49 C50 P5S sing 507 n n C49 H49 P5S sing 508 n n C49 H49A P5S sing 509 n n C50 C51 P5S sing 510 n n C50 H50 P5S sing 511 n n C50 H50A P5S sing 512 n n C51 C52 P5S sing 513 n n C51 H51 P5S sing 514 n n C51 H51A P5S sing 515 n n C53 C52 P5S sing 516 n n C52 H52 P5S sing 517 n n C52 H52A P5S sing 518 n n C53 C54 P5S sing 519 n n C53 H53 P5S sing 520 n n C53 H53A P5S sing 521 n n C55 C54 P5S sing 522 n n C54 H54 P5S sing 523 n n C54 H54A P5S sing 524 n n C55 C56 P5S sing 525 n n C55 H55 P5S sing 526 n n C55 H55A P5S sing 527 n n C56 H56 P5S sing 528 n n C56 H56A P5S sing 529 n n C56 H56B P5S sing 530 n n OXT HXT P5S sing 531 n n # _atom_sites.entry_id 7W9M _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 5 9SR A 1 2001 1901 9SR TTX . G 6 NAG A 1 2002 2006 NAG NAG . H 6 NAG A 1 2003 2009 NAG NAG . I 7 P5S A 1 2004 2012 P5S P5S . J 8 Y01 A 1 2005 2015 Y01 Y01 . K 8 Y01 A 1 2006 2016 Y01 Y01 . L 8 Y01 A 1 2007 2017 Y01 Y01 . M 8 Y01 A 1 2008 2020 Y01 Y01 . N 6 NAG A 1 2009 2021 NAG NAG . O 8 Y01 A 1 2010 2022 Y01 Y01 . P 6 NAG B 1 301 301 NAG NAG . Q 6 NAG B 1 302 302 NAG NAG . R 6 NAG B 1 303 303 NAG NAG . S 9 LPE B 1 304 306 LPE LPE . # 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 . . . I 7 111.581 88.702 108.159 1 20 ? C P5S 2004 A 1 HETATM 2 N N P5S . . . I 7 110.478 90.541 109.368 1 20 ? N P5S 2004 A 1 HETATM 3 O O P5S . . . I 7 112.428 88.225 107.431 1 20 ? O P5S 2004 A 1 HETATM 4 C C1 P5S . . . I 7 117.222 89.741 108.881 1 20 ? C1 P5S 2004 A 1 HETATM 5 C C2 P5S . . . I 7 117.055 88.623 109.891 1 20 ? C2 P5S 2004 A 1 HETATM 6 C C3 P5S . . . I 7 116.208 89.152 111.034 1 20 ? C3 P5S 2004 A 1 HETATM 7 C CA P5S . . . I 7 111.762 90.059 108.808 1 20 ? CA P5S 2004 A 1 HETATM 8 C CB P5S . . . I 7 112.851 90.052 109.894 1 20 ? CB P5S 2004 A 1 HETATM 9 O OG P5S . . . I 7 113.732 88.941 109.827 1 20 ? OG P5S 2004 A 1 HETATM 10 P P12 P5S . . . I 7 113.925 87.861 111.004 1 20 ? P12 P5S 2004 A 1 HETATM 11 O O13 P5S . . . I 7 112.901 87.954 112.044 1 20 1 O13 P5S 2004 A 1 HETATM 12 O O15 P5S . . . I 7 113.86 86.385 110.379 1 20 ? O15 P5S 2004 A 1 HETATM 13 O O16 P5S . . . I 7 115.384 88.128 111.582 1 20 ? O16 P5S 2004 A 1 HETATM 14 O O19 P5S . . . I 7 118.18 90.698 109.307 1 20 ? O19 P5S 2004 A 1 HETATM 15 O O37 P5S . . . I 7 118.322 88.216 110.392 1 20 ? O37 P5S 2004 A 1 HETATM 16 C C38 P5S . . . I 7 118.946 87.237 109.55 1 20 ? C38 P5S 2004 A 1 HETATM 17 C C39 P5S . . . I 7 120.437 87.201 109.445 1 20 ? C39 P5S 2004 A 1 HETATM 18 C C40 P5S . . . I 7 120.912 85.943 110.135 1 20 ? C40 P5S 2004 A 1 HETATM 19 C C41 P5S . . . I 7 121.677 86.305 111.385 1 20 ? C41 P5S 2004 A 1 HETATM 20 C C42 P5S . . . I 7 122.65 85.195 111.678 1 20 ? C42 P5S 2004 A 1 HETATM 21 C C43 P5S . . . I 7 122.798 85.085 113.175 1 20 ? C43 P5S 2004 A 1 HETATM 22 C C44 P5S . . . I 7 121.989 83.934 113.729 1 20 ? C44 P5S 2004 A 1 HETATM 23 C C45 P5S . . . I 7 121.868 84.105 115.227 1 20 ? C45 P5S 2004 A 1 HETATM 24 C C46 P5S . . . I 7 120.594 83.449 115.718 1 20 ? C46 P5S 2004 A 1 HETATM 25 O O47 P5S . . . I 7 118.263 86.443 108.935 1 20 ? O47 P5S 2004 A 1 HETATM 26 C C48 P5S . . . I 7 120.151 83.998 117.06 1 20 ? C48 P5S 2004 A 1 HETATM 27 C C49 P5S . . . I 7 121.026 83.448 118.165 1 20 ? C49 P5S 2004 A 1 HETATM 28 C C50 P5S . . . I 7 120.207 82.661 119.168 1 20 ? C50 P5S 2004 A 1 HETATM 29 C C51 P5S . . . I 7 120.555 83.048 120.587 1 20 ? C51 P5S 2004 A 1 HETATM 30 C C52 P5S . . . I 7 120.202 81.89 121.492 1 20 ? C52 P5S 2004 A 1 HETATM 31 C C53 P5S . . . I 7 119.8 82.39 122.868 1 20 ? C53 P5S 2004 A 1 HETATM 32 C C54 P5S . . . I 7 120.571 81.676 123.966 1 20 ? C54 P5S 2004 A 1 HETATM 33 C C55 P5S . . . I 7 119.77 80.555 124.613 1 20 ? C55 P5S 2004 A 1 HETATM 34 C C56 P5S . . . I 7 118.403 81.011 125.073 1 20 ? C56 P5S 2004 A 1 HETATM 35 O OXT P5S . . . I 7 110.492 87.979 108.287 1 20 ? OXT P5S 2004 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 35 #