data_1F88 # _model_server_result.job_id T8KBHA5U69jRankvzpbGjQ _model_server_result.datetime_utc '2024-11-23 11:55:28' _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 1f88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":978}' # _entry.id 1F88 # _exptl.entry_id 1F88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 2 _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 1F88 _cell.length_a 97.246 _cell.length_b 97.246 _cell.length_c 149.544 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1F88 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 dimeric 2 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 A,C,D,G,H,I,J,K,L,S 2 1 B,E,F,M,N,O,P,Q,R,T 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 L N N ? 6 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 MAN 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 C NAG 1 C 1 NAG ? 501 NAG 2 n C NAG 2 C 2 NAG ? 502 NAG 2 n D NAG 1 D 1 NAG ? 701 NAG 2 n D NAG 2 D 2 NAG ? 702 NAG 3 n E NAG 1 E 1 NAG ? 601 NAG 3 n E NAG 2 E 2 NAG ? 602 NAG 3 n E MAN 3 E 3 MAN ? 603 MAN 2 n F NAG 1 F 1 NAG ? 801 NAG 2 n F NAG 2 F 2 NAG ? 802 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 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 187 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 2 A ASN 2 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A ND2 ASN 15 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A NZ LYS 296 A LYS 296 1_555 L C15 RET . A RET 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B ND2 ASN 2 B ASN 2 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 B ND2 ASN 15 B ASN 15 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B NZ LYS 296 B LYS 296 1_555 R C15 RET . B RET 978 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale10 E O4 NAG . E NAG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? metalc ? metalc1 A O ALA 132 A ALA 132 1_555 H HG HG . A HG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.388 ? metalc ? metalc2 A OE2 GLU 196 A GLU 196 2_655 P ZN ZN . B ZN 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc3 A OE1 GLU 196 A GLU 196 2_655 P ZN ZN . B ZN 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc4 A OE1 GLU 201 A GLU 201 1_555 J ZN ZN . A ZN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc5 A SG CYS 222 A CYS 222 1_555 H HG HG . A HG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc6 A N TYR 223 A TYR 223 1_555 H HG HG . A HG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.473 ? metalc ? metalc7 A SG CYS 264 A CYS 264 1_555 G HG HG . A HG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc8 A NE2 GLN 279 A GLN 279 1_555 J ZN ZN . A ZN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc9 A OG1 THR 297 A THR 297 1_555 G HG HG . A HG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? metalc ? metalc10 A O GLN 312 A GLN 312 1_555 I HG HG . A HG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.295 ? metalc ? metalc11 A SG CYS 316 A CYS 316 1_555 I HG HG . A HG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc12 B ND1 HIS 65 B HIS 65 1_555 O HG HG . B HG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.468 ? metalc ? metalc13 B O ALA 132 B ALA 132 1_555 N HG HG . B HG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.218 ? metalc ? metalc14 B NE2 HIS 195 B HIS 195 1_555 Q ZN ZN . B ZN 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc15 B SG CYS 222 B CYS 222 1_555 N HG HG . B HG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc16 B O CYS 222 B CYS 222 1_555 N HG HG . B HG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.367 ? metalc ? metalc17 B N TYR 223 B TYR 223 1_555 N HG HG . B HG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.521 ? metalc ? metalc18 B O ALA 260 B ALA 260 1_555 M HG HG . B HG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? metalc ? metalc19 B SG CYS 264 B CYS 264 1_555 M HG HG . B HG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc20 B OG1 THR 297 B THR 297 1_555 M HG HG . B HG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.411 ? metalc ? metalc21 B SG CYS 316 B CYS 316 1_555 O HG HG . B HG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 RET sing 331 n n C1 C6 RET sing 332 n n C1 C16 RET sing 333 n n C1 C17 RET sing 334 n n C2 C3 RET sing 335 n n C2 H21 RET sing 336 n n C2 H22 RET sing 337 n n C3 C4 RET sing 338 n n C3 H31 RET sing 339 n n C3 H32 RET sing 340 n n C4 C5 RET sing 341 n n C4 H41 RET sing 342 n n C4 H42 RET sing 343 n n C5 C6 RET doub 344 n n C5 C18 RET sing 345 n n C6 C7 RET sing 346 n n C7 C8 RET doub 347 e n C7 H7 RET sing 348 n n C8 C9 RET sing 349 n n C8 H8 RET sing 350 n n C9 C10 RET doub 351 e n C9 C19 RET sing 352 n n C10 C11 RET sing 353 n n C10 H10 RET sing 354 n n C11 C12 RET doub 355 e n C11 H11 RET sing 356 n n C12 C13 RET sing 357 n n C12 H12 RET sing 358 n n C13 C14 RET doub 359 e n C13 C20 RET sing 360 n n C14 C15 RET sing 361 n n C14 H14 RET sing 362 n n C15 O1 RET doub 363 n n C15 H15 RET sing 364 n n C16 H161 RET sing 365 n n C16 H162 RET sing 366 n n C16 H163 RET sing 367 n n C17 H171 RET sing 368 n n C17 H172 RET sing 369 n n C17 H173 RET sing 370 n n C18 H181 RET sing 371 n n C18 H182 RET sing 372 n n C18 H183 RET sing 373 n n C19 H191 RET sing 374 n n C19 H192 RET sing 375 n n C19 H193 RET sing 376 n n C20 H201 RET sing 377 n n C20 H202 RET sing 378 n n C20 H203 RET sing 379 n n # _atom_sites.entry_id 1F88 _atom_sites.fract_transf_matrix[1][1] 0.010283 _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] 0.010283 _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] 0.006687 _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 G 4 HG A 1 901 901 HG HG2 . H 4 HG A 1 903 903 HG HG2 . I 4 HG A 1 905 905 HG HG2 . J 5 ZN A 1 907 907 ZN ZN2 . K 5 ZN A 1 910 910 ZN ZN2 . L 6 RET A 1 977 296 RET RET . M 4 HG B 1 902 902 HG HG2 . N 4 HG B 1 904 904 HG HG2 . O 4 HG B 1 906 906 HG HG2 . P 5 ZN B 1 908 908 ZN ZN2 . Q 5 ZN B 1 909 909 ZN ZN2 . R 6 RET B 1 978 296 RET RET . S 7 HOH A 1 950 950 HOH WAT . S 7 HOH A 2 952 952 HOH WAT . S 7 HOH A 3 953 953 HOH WAT . S 7 HOH A 4 958 958 HOH WAT . S 7 HOH A 5 959 959 HOH WAT . S 7 HOH A 6 962 962 HOH WAT . S 7 HOH A 7 963 963 HOH WAT . S 7 HOH A 8 964 964 HOH WAT . S 7 HOH A 9 965 965 HOH WAT . S 7 HOH A 10 966 966 HOH WAT . S 7 HOH A 11 967 967 HOH WAT . S 7 HOH A 12 968 968 HOH WAT . S 7 HOH A 13 970 970 HOH WAT . S 7 HOH A 14 971 971 HOH WAT . S 7 HOH A 15 972 972 HOH WAT . S 7 HOH A 16 974 974 HOH WAT . T 7 HOH B 1 951 951 HOH WAT . T 7 HOH B 2 954 954 HOH WAT . T 7 HOH B 3 955 955 HOH WAT . T 7 HOH B 4 956 956 HOH WAT . T 7 HOH B 5 957 957 HOH WAT . T 7 HOH B 6 960 960 HOH WAT . T 7 HOH B 7 961 961 HOH WAT . T 7 HOH B 8 969 969 HOH WAT . T 7 HOH B 9 973 973 HOH WAT . T 7 HOH B 10 975 975 HOH WAT . T 7 HOH B 11 976 976 HOH WAT . # 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 RET . . . R 6 33.234 8.591 25.798 1 34.05 ? C1 RET 978 B 1 HETATM 2 C C2 RET . . . R 6 31.995 8.387 24.968 1 33.95 ? C2 RET 978 B 1 HETATM 3 C C3 RET . . . R 6 32.242 8.645 23.513 1 33.45 ? C3 RET 978 B 1 HETATM 4 C C4 RET . . . R 6 32.72 10.104 23.258 1 33.69 ? C4 RET 978 B 1 HETATM 5 C C5 RET . . . R 6 33.717 10.591 24.302 1 34.43 ? C5 RET 978 B 1 HETATM 6 C C6 RET . . . R 6 33.938 9.9 25.443 1 34.95 ? C6 RET 978 B 1 HETATM 7 C C7 RET . . . R 6 34.915 10.362 26.451 1 36.11 ? C7 RET 978 B 1 HETATM 8 C C8 RET . . . R 6 36.195 10.507 26.017 1 36.04 ? C8 RET 978 B 1 HETATM 9 C C9 RET . . . R 6 37.41 10.945 26.731 1 36.99 ? C9 RET 978 B 1 HETATM 10 C C10 RET . . . R 6 38.639 11.044 26.15 1 35.86 ? C10 RET 978 B 1 HETATM 11 C C11 RET . . . R 6 39.898 11.497 26.8 1 34.76 ? C11 RET 978 B 1 HETATM 12 C C12 RET . . . R 6 41.161 11.577 26.282 1 29.43 ? C12 RET 978 B 1 HETATM 13 C C13 RET . . . R 6 41.797 11.249 24.973 1 27.49 ? C13 RET 978 B 1 HETATM 14 C C14 RET . . . R 6 42.936 11.815 24.56 1 26.08 ? C14 RET 978 B 1 HETATM 15 C C15 RET . . . R 6 43.597 11.506 23.277 1 24.41 ? C15 RET 978 B 1 HETATM 16 C C16 RET . . . R 6 32.82 8.596 27.249 1 33.42 ? C16 RET 978 B 1 HETATM 17 C C17 RET . . . R 6 34.191 7.414 25.6 1 34.55 ? C17 RET 978 B 1 HETATM 18 C C18 RET . . . R 6 34.427 11.893 23.923 1 32.56 ? C18 RET 978 B 1 HETATM 19 C C19 RET . . . R 6 37.148 11.266 28.168 1 34.94 ? C19 RET 978 B 1 HETATM 20 C C20 RET . . . R 6 41.098 10.221 24.149 1 29.8 ? C20 RET 978 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #