data_7ZDI # _model_server_result.job_id TU5cnBuyY5NiNQzsffrtsA _model_server_result.datetime_utc '2025-03-06 08:51:59' _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 7zdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"WA","auth_seq_id":103}' # _entry.id 7ZDI # _exptl.entry_id 7ZDI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 554.888 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-Dihydro-psi,psi-caroten-1-ol _entity.pdbx_number_of_molecules 9 _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 7ZDI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZDI _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 nonadecameric _pdbx_struct_assembly.oligomeric_count 19 _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,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB _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 ? 5 V N N ? 5 W N N ? 5 KA N N ? 5 OA N N ? 5 RA N N ? 5 SA N N ? 5 WA N N ? 5 AB N N ? 5 EB 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 covale ? covale1 A C CXM 1 A CXM 1 1_555 A N ASN 2 A ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 D C CXM 1 C CXM 1 1_555 D N ASN 2 C ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 F C CXM 1 E CXM 1 1_555 F N ASN 2 E ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 H C CXM 1 G CXM 1 1_555 H N ASN 2 G ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 J C CXM 1 I CXM 1 1_555 J N ASN 2 I ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 L C CXM 1 K CXM 1 1_555 L N ASN 2 K ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 N C CXM 1 M CXM 1 1_555 N N ASN 2 M ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 P C CXM 1 O CXM 1 1_555 P N ASN 2 O ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 R C CXM 1 Q CXM 1 1_555 R N ASN 2 Q ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A ON1 CXM 1 A CXM 1 1_555 U MG BCL . A BCL 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc2 C O SER 9 S SER 9 1_555 Z MG BCL . S BCL 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 C O SER 25 S SER 25 1_555 AA MG BCL . S BCL 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc4 C O SER 41 S SER 41 1_555 BA MG BCL . S BCL 1704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc5 C O SER 57 S SER 57 1_555 CA MG BCL . S BCL 1705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc6 C O SER 73 S SER 73 1_555 DA MG BCL . S BCL 1706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc7 C O SER 89 S SER 89 1_555 Y MG BCL . S BCL 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc8 D ON1 CXM 1 C CXM 1 1_555 EA MG BCL . C BCL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc9 F ON1 CXM 1 E CXM 1 1_555 IA MG BCL . E BCL 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc10 H ON1 CXM 1 G CXM 1 1_555 MA MG BCL . G BCL 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc11 J ON1 CXM 1 I CXM 1 1_555 PA MG BCL . I BCL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc12 L ON1 CXM 1 K CXM 1 1_555 UA MG BCL . K BCL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc13 N ON1 CXM 1 M CXM 1 1_555 YA MG BCL . M BCL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc14 P ON1 CXM 1 O CXM 1 1_555 DB MG BCL . O BCL 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc15 R ON1 CXM 1 Q CXM 1 1_555 GB MG BCL . Q BCL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? # _chem_comp.formula 'C40 H58 O' _chem_comp.formula_weight 554.888 _chem_comp.id IRM _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-Dihydro-psi,psi-caroten-1-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Rhodopin;(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-6,8,10,12,14,16,18,20,22,24,26,30-dodecaen-2-ol # 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 O32 C1 IRM sing 328 n n C31 C1 IRM sing 329 n n C1 C30 IRM sing 330 n n C1 C2 IRM sing 331 n n C2 C3 IRM sing 332 n n C3 C4 IRM sing 333 n n C4 C5 IRM sing 334 n n C5 C33 IRM sing 335 n n C5 C6 IRM doub 336 e n C6 C7 IRM sing 337 n n C7 C8 IRM doub 338 e n C8 C9 IRM sing 339 n n C9 C34 IRM sing 340 n n C9 C10 IRM doub 341 e n C10 C11 IRM sing 342 n n C11 C12 IRM doub 343 e n C12 C13 IRM sing 344 n n C13 C14 IRM doub 345 e n C13 C35 IRM sing 346 n n C14 C15 IRM sing 347 n n C15 C16 IRM doub 348 e n C16 C17 IRM sing 349 n n C36 C18 IRM sing 350 n n C17 C18 IRM doub 351 e n C18 C19 IRM sing 352 n n C19 C20 IRM doub 353 e n C20 C21 IRM sing 354 n n C37 C22 IRM sing 355 n n C21 C22 IRM doub 356 e n C22 C23 IRM sing 357 n n C23 C24 IRM doub 358 e n C24 C25 IRM sing 359 n n C25 C26 IRM doub 360 e n C38 C26 IRM sing 361 n n C26 C27 IRM sing 362 n n C27 C28 IRM sing 363 n n C28 C29 IRM sing 364 n n C29 C39 IRM doub 365 n n C41 C39 IRM sing 366 n n C39 C40 IRM sing 367 n n C10 H1 IRM sing 368 n n C11 H2 IRM sing 369 n n C12 H3 IRM sing 370 n n C14 H4 IRM sing 371 n n C15 H5 IRM sing 372 n n C16 H6 IRM sing 373 n n C17 H7 IRM sing 374 n n C19 H8 IRM sing 375 n n C2 H9 IRM sing 376 n n C2 H10 IRM sing 377 n n C20 H11 IRM sing 378 n n C21 H12 IRM sing 379 n n C23 H13 IRM sing 380 n n C24 H14 IRM sing 381 n n C25 H15 IRM sing 382 n n C27 H16 IRM sing 383 n n C27 H17 IRM sing 384 n n C28 H18 IRM sing 385 n n C28 H19 IRM sing 386 n n C29 H20 IRM sing 387 n n C3 H21 IRM sing 388 n n C3 H22 IRM sing 389 n n C30 H23 IRM sing 390 n n C30 H24 IRM sing 391 n n C30 H25 IRM sing 392 n n C31 H26 IRM sing 393 n n C31 H27 IRM sing 394 n n C31 H28 IRM sing 395 n n C33 H29 IRM sing 396 n n C33 H30 IRM sing 397 n n C33 H31 IRM sing 398 n n C34 H32 IRM sing 399 n n C34 H33 IRM sing 400 n n C34 H34 IRM sing 401 n n C35 H35 IRM sing 402 n n C35 H36 IRM sing 403 n n C35 H37 IRM sing 404 n n C36 H38 IRM sing 405 n n C36 H39 IRM sing 406 n n C36 H40 IRM sing 407 n n C37 H41 IRM sing 408 n n C37 H42 IRM sing 409 n n C37 H43 IRM sing 410 n n C38 H44 IRM sing 411 n n C38 H45 IRM sing 412 n n C38 H46 IRM sing 413 n n C4 H47 IRM sing 414 n n C4 H48 IRM sing 415 n n C40 H49 IRM sing 416 n n C40 H50 IRM sing 417 n n C40 H51 IRM sing 418 n n C41 H52 IRM sing 419 n n C41 H53 IRM sing 420 n n C41 H54 IRM sing 421 n n C6 H55 IRM sing 422 n n C7 H56 IRM sing 423 n n C8 H57 IRM sing 424 n n O32 H58 IRM sing 425 n n # _atom_sites.entry_id 7ZDI _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 T 4 BCL A 1 101 1502 BCL BCL . U 4 BCL A 1 102 1702 BCL BCL . V 5 IRM A 1 103 1801 IRM RDP . W 5 IRM B 1 1801 1801 IRM RDP . X 4 BCL B 1 1802 1602 BCL BCL . Y 4 BCL S 1 1701 1701 BCL BCL . Z 4 BCL S 1 1702 1701 BCL BCL . AA 4 BCL S 1 1703 1701 BCL BCL . BA 4 BCL S 1 1704 1701 BCL BCL . CA 4 BCL S 1 1705 1701 BCL BCL . DA 4 BCL S 1 1706 1701 BCL BCL . EA 4 BCL C 1 101 1702 BCL BCL . FA 4 BCL C 1 102 1502 BCL BCL . GA 4 BCL D 1 101 1602 BCL BCL . HA 4 BCL E 1 101 1502 BCL BCL . IA 4 BCL E 1 102 1702 BCL BCL . JA 4 BCL F 1 101 1602 BCL BCL . KA 5 IRM F 1 102 1801 IRM RDP . LA 4 BCL G 1 101 1502 BCL BCL . MA 4 BCL G 1 102 1702 BCL BCL . NA 4 BCL H 1 101 1602 BCL BCL . OA 5 IRM H 1 102 1801 IRM RDP . PA 4 BCL I 1 101 1702 BCL BCL . QA 4 BCL I 1 102 1502 BCL BCL . RA 5 IRM I 1 103 1801 IRM RDP . SA 5 IRM J 1 1801 1801 IRM RDP . TA 4 BCL J 1 1802 1602 BCL BCL . UA 4 BCL K 1 101 1702 BCL BCL . VA 4 BCL K 1 102 1502 BCL BCL . WA 5 IRM K 1 103 1801 IRM RDP . XA 4 BCL L 1 101 1602 BCL BCL . YA 4 BCL M 1 101 1702 BCL BCL . ZA 4 BCL M 1 102 1502 BCL BCL . AB 5 IRM M 1 103 1801 IRM RDP . BB 4 BCL N 1 101 1602 BCL BCL . CB 4 BCL O 1 101 1502 BCL BCL . DB 4 BCL O 1 102 1702 BCL BCL . EB 5 IRM O 1 103 1801 IRM RDP . FB 4 BCL P 1 101 1602 BCL BCL . GB 4 BCL Q 1 101 1702 BCL BCL . HB 4 BCL Q 1 102 1502 BCL BCL . IB 4 BCL R 1 101 1602 BCL BCL . # 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 IRM . . . WA 5 124.116 97.288 118.86 1 35.93 ? C1 IRM 103 K 1 HETATM 2 C C10 IRM . . . WA 5 122.75 98.318 108.358 1 24.07 ? C10 IRM 103 K 1 HETATM 3 C C11 IRM . . . WA 5 122.974 98.369 106.951 1 23.9 ? C11 IRM 103 K 1 HETATM 4 C C12 IRM . . . WA 5 122.67 99.44 106.212 1 24.25 ? C12 IRM 103 K 1 HETATM 5 C C13 IRM . . . WA 5 122.816 99.589 104.775 1 23.52 ? C13 IRM 103 K 1 HETATM 6 C C14 IRM . . . WA 5 122.47 100.766 104.204 1 24.46 ? C14 IRM 103 K 1 HETATM 7 C C15 IRM . . . WA 5 122.455 101.1 102.819 1 24.48 ? C15 IRM 103 K 1 HETATM 8 C C16 IRM . . . WA 5 122.06 102.313 102.393 1 25.66 ? C16 IRM 103 K 1 HETATM 9 C C17 IRM . . . WA 5 121.897 102.705 101.036 1 26.01 ? C17 IRM 103 K 1 HETATM 10 C C18 IRM . . . WA 5 121.405 103.882 100.585 1 27.52 ? C18 IRM 103 K 1 HETATM 11 C C19 IRM . . . WA 5 121.042 104.025 99.188 1 27.86 ? C19 IRM 103 K 1 HETATM 12 C C2 IRM . . . WA 5 123.091 96.953 117.781 1 32.3 ? C2 IRM 103 K 1 HETATM 13 C C20 IRM . . . WA 5 120.332 105.029 98.666 1 27.65 ? C20 IRM 103 K 1 HETATM 14 C C21 IRM . . . WA 5 119.934 105.139 97.303 1 27.42 ? C21 IRM 103 K 1 HETATM 15 C C22 IRM . . . WA 5 119.13 106.083 96.76 1 26.51 ? C22 IRM 103 K 1 HETATM 16 C C23 IRM . . . WA 5 118.788 106.005 95.353 1 24.02 ? C23 IRM 103 K 1 HETATM 17 C C24 IRM . . . WA 5 117.91 106.773 94.7 1 21.59 ? C24 IRM 103 K 1 HETATM 18 C C25 IRM . . . WA 5 117.686 106.7 93.302 1 20.18 ? C25 IRM 103 K 1 HETATM 19 C C26 IRM . . . WA 5 116.784 107.428 92.632 1 17.55 ? C26 IRM 103 K 1 HETATM 20 C C27 IRM . . . WA 5 116.722 107.412 91.128 1 17.67 ? C27 IRM 103 K 1 HETATM 21 C C28 IRM . . . WA 5 115.83 106.314 90.539 1 17.56 ? C28 IRM 103 K 1 HETATM 22 C C29 IRM . . . WA 5 116 106.253 89.053 1 17.11 ? C29 IRM 103 K 1 HETATM 23 C C3 IRM . . . WA 5 123.626 96.806 116.361 1 31.12 ? C3 IRM 103 K 1 HETATM 24 C C30 IRM . . . WA 5 124.768 98.634 118.601 1 33.6 ? C30 IRM 103 K 1 HETATM 25 C C31 IRM . . . WA 5 123.487 97.251 120.243 1 39.77 ? C31 IRM 103 K 1 HETATM 26 C C33 IRM . . . WA 5 123.928 94.871 113.857 1 27.83 ? C33 IRM 103 K 1 HETATM 27 C C34 IRM . . . WA 5 123.699 96.03 108.765 1 25.52 ? C34 IRM 103 K 1 HETATM 28 C C35 IRM . . . WA 5 123.357 98.427 103.993 1 24.52 ? C35 IRM 103 K 1 HETATM 29 C C36 IRM . . . WA 5 121.142 105.046 101.496 1 27.49 ? C36 IRM 103 K 1 HETATM 30 C C37 IRM . . . WA 5 118.57 107.228 97.556 1 25.26 ? C37 IRM 103 K 1 HETATM 31 C C38 IRM . . . WA 5 115.756 108.288 93.31 1 16.7 ? C38 IRM 103 K 1 HETATM 32 C C39 IRM . . . WA 5 115.228 105.649 88.166 1 21.44 ? C39 IRM 103 K 1 HETATM 33 C C4 IRM . . . WA 5 122.543 96.346 115.399 1 30 ? C4 IRM 103 K 1 HETATM 34 C C40 IRM . . . WA 5 115.531 105.661 86.699 1 22.32 ? C40 IRM 103 K 1 HETATM 35 C C41 IRM . . . WA 5 113.98 104.906 88.541 1 21.77 ? C41 IRM 103 K 1 HETATM 36 C C5 IRM . . . WA 5 123.041 96.074 114.002 1 28.34 ? C5 IRM 103 K 1 HETATM 37 C C6 IRM . . . WA 5 122.723 96.874 112.976 1 28.73 ? C6 IRM 103 K 1 HETATM 38 C C7 IRM . . . WA 5 123.092 96.644 111.618 1 26.92 ? C7 IRM 103 K 1 HETATM 39 C C8 IRM . . . WA 5 122.771 97.478 110.624 1 25.54 ? C8 IRM 103 K 1 HETATM 40 C C9 IRM . . . WA 5 123.061 97.314 109.211 1 24.05 ? C9 IRM 103 K 1 HETATM 41 O O32 IRM . . . WA 5 125.151 96.287 118.819 1 38.47 ? O32 IRM 103 K 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 41 #