data_6RF0 # _model_server_result.job_id Z8ZyB_VaweKWOzCrNsw4KA _model_server_result.datetime_utc '2024-11-16 08:53:15' _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 6rf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":306}' # _entry.id 6RF0 # _exptl.entry_id 6RF0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 5 _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 6RF0 _cell.length_a 128.184 _cell.length_b 239.719 _cell.length_c 131.909 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 J N N ? 5 P N N ? 5 U N N ? 5 Z N N ? 5 DA 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 NZ LYS 255 A LYS 255 1_555 J C15 RET . A RET 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 B NZ LYS 255 B LYS 255 1_555 P C15 RET . B RET 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 C NZ LYS 255 C LYS 255 1_555 U C15 RET . C RET 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale4 D NZ LYS 255 D LYS 255 1_555 Z C15 RET . D RET 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 E NZ LYS 255 E LYS 255 1_555 DA C15 RET . E RET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? metalc ? metalc1 A OH TYR 25 A TYR 25 1_555 F NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc2 A O THR 83 A THR 83 1_555 F NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc3 A O PHE 86 A PHE 86 1_555 F NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc4 A OD1 ASP 102 A ASP 102 1_555 I NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc5 A OD2 ASP 102 A ASP 102 1_555 I NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc6 F NA NA . A NA 301 1_555 B OD1 ASP 102 B ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc7 F NA NA . A NA 301 1_555 B OD2 ASP 102 B ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc8 I NA NA . A NA 304 1_555 E OH TYR 25 E TYR 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc9 I NA NA . A NA 304 1_555 E O THR 83 E THR 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc10 I NA NA . A NA 304 1_555 E O PHE 86 E PHE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc11 B OH TYR 25 B TYR 25 1_555 K NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc12 B O THR 83 B THR 83 1_555 K NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc13 B O PHE 86 B PHE 86 1_555 K NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc14 K NA NA . B NA 301 1_555 C OD1 ASP 102 C ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc15 K NA NA . B NA 301 1_555 C OD2 ASP 102 C ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc16 C OH TYR 25 C TYR 25 1_555 Q NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc17 C O THR 83 C THR 83 1_555 Q NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc18 C O PHE 86 C PHE 86 1_555 Q NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc19 Q NA NA . C NA 301 1_555 D OD1 ASP 102 D ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc20 Q NA NA . C NA 301 1_555 D OD2 ASP 102 D ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc21 D OH TYR 25 D TYR 25 1_555 V NA NA . D NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.037 ? metalc ? metalc22 D O THR 83 D THR 83 1_555 V NA NA . D NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc23 D O PHE 86 D PHE 86 1_555 V NA NA . D NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc24 V NA NA . D NA 301 1_555 E OD1 ASP 102 E ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc25 V NA NA . D NA 301 1_555 E OD2 ASP 102 E ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? # _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 389 n n C1 C6 RET sing 390 n n C1 C16 RET sing 391 n n C1 C17 RET sing 392 n n C2 C3 RET sing 393 n n C2 H21 RET sing 394 n n C2 H22 RET sing 395 n n C3 C4 RET sing 396 n n C3 H31 RET sing 397 n n C3 H32 RET sing 398 n n C4 C5 RET sing 399 n n C4 H41 RET sing 400 n n C4 H42 RET sing 401 n n C5 C6 RET doub 402 n n C5 C18 RET sing 403 n n C6 C7 RET sing 404 n n C7 C8 RET doub 405 e n C7 H7 RET sing 406 n n C8 C9 RET sing 407 n n C8 H8 RET sing 408 n n C9 C10 RET doub 409 e n C9 C19 RET sing 410 n n C10 C11 RET sing 411 n n C10 H10 RET sing 412 n n C11 C12 RET doub 413 e n C11 H11 RET sing 414 n n C12 C13 RET sing 415 n n C12 H12 RET sing 416 n n C13 C14 RET doub 417 e n C13 C20 RET sing 418 n n C14 C15 RET sing 419 n n C14 H14 RET sing 420 n n C15 O1 RET doub 421 n n C15 H15 RET sing 422 n n C16 H161 RET sing 423 n n C16 H162 RET sing 424 n n C16 H163 RET sing 425 n n C17 H171 RET sing 426 n n C17 H172 RET sing 427 n n C17 H173 RET sing 428 n n C18 H181 RET sing 429 n n C18 H182 RET sing 430 n n C18 H183 RET sing 431 n n C19 H191 RET sing 432 n n C19 H192 RET sing 433 n n C19 H193 RET sing 434 n n C20 H201 RET sing 435 n n C20 H202 RET sing 436 n n C20 H203 RET sing 437 n n # _atom_sites.entry_id 6RF0 _atom_sites.fract_transf_matrix[1][1] 0.007801 _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] 0.004172 _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] 0.007581 _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 2 NA A 1 301 301 NA NA . G 3 OLC A 1 302 401 OLC OLC . H 4 LFA A 1 303 501 LFA LFA . I 2 NA A 1 304 301 NA NA . J 5 RET A 1 305 255 RET LYR . K 2 NA B 1 301 301 NA NA . L 4 LFA B 1 302 303 LFA LFA . M 4 LFA B 1 303 304 LFA LFA . N 3 OLC B 1 304 401 OLC OLC . O 4 LFA B 1 305 501 LFA LFA . P 5 RET B 1 306 255 RET LYR . Q 2 NA C 1 301 301 NA NA . R 4 LFA C 1 302 303 LFA LFA . S 3 OLC C 1 303 401 OLC OLC . T 4 LFA C 1 304 501 LFA LFA . U 5 RET C 1 305 255 RET LYR . V 2 NA D 1 301 301 NA NA . W 4 LFA D 1 302 303 LFA LFA . X 3 OLC D 1 303 401 OLC OLC . Y 4 LFA D 1 304 501 LFA LFA . Z 5 RET D 1 305 255 RET LYR . AA 4 LFA E 1 301 302 LFA LFA . BA 3 OLC E 1 302 401 OLC OLC . CA 4 LFA E 1 303 601 LFA LFA . DA 5 RET E 1 304 255 RET LYR . EA 6 HOH A 1 401 9 HOH HOH . EA 6 HOH A 2 402 28 HOH HOH . EA 6 HOH A 3 403 3 HOH HOH . EA 6 HOH A 4 404 32 HOH HOH . EA 6 HOH A 5 405 23 HOH HOH . EA 6 HOH A 6 406 10 HOH HOH . EA 6 HOH A 7 407 2 HOH HOH . EA 6 HOH A 8 408 35 HOH HOH . EA 6 HOH A 9 409 41 HOH HOH . FA 6 HOH B 1 401 33 HOH HOH . FA 6 HOH B 2 402 21 HOH HOH . FA 6 HOH B 3 403 42 HOH HOH . FA 6 HOH B 4 404 12 HOH HOH . FA 6 HOH B 5 405 36 HOH HOH . FA 6 HOH B 6 406 24 HOH HOH . GA 6 HOH C 1 401 29 HOH HOH . GA 6 HOH C 2 402 14 HOH HOH . GA 6 HOH C 3 403 13 HOH HOH . GA 6 HOH C 4 404 22 HOH HOH . GA 6 HOH C 5 405 8 HOH HOH . GA 6 HOH C 6 406 16 HOH HOH . GA 6 HOH C 7 407 15 HOH HOH . GA 6 HOH C 8 408 34 HOH HOH . GA 6 HOH C 9 409 27 HOH HOH . GA 6 HOH C 10 410 37 HOH HOH . HA 6 HOH D 1 401 30 HOH HOH . HA 6 HOH D 2 402 7 HOH HOH . HA 6 HOH D 3 403 11 HOH HOH . HA 6 HOH D 4 404 19 HOH HOH . HA 6 HOH D 5 405 38 HOH HOH . HA 6 HOH D 6 406 39 HOH HOH . HA 6 HOH D 7 407 6 HOH HOH . HA 6 HOH D 8 408 40 HOH HOH . HA 6 HOH D 9 409 17 HOH HOH . IA 6 HOH E 1 401 31 HOH HOH . IA 6 HOH E 2 402 20 HOH HOH . IA 6 HOH E 3 403 18 HOH HOH . IA 6 HOH E 4 404 25 HOH HOH . IA 6 HOH E 5 405 5 HOH HOH . IA 6 HOH E 6 406 26 HOH HOH . IA 6 HOH E 7 407 1 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 C1 RET . . . P 5 -8.79 -28.002 20.696 1 57.28 ? C1 RET 306 B 1 HETATM 2 C C2 RET . . . P 5 -8.476 -26.799 21.571 1 56.08 ? C2 RET 306 B 1 HETATM 3 C C3 RET . . . P 5 -7 -26.456 21.486 1 53.2 ? C3 RET 306 B 1 HETATM 4 C C4 RET . . . P 5 -6.191 -27.571 22.121 1 54.4 ? C4 RET 306 B 1 HETATM 5 C C5 RET . . . P 5 -6.644 -28.917 21.612 1 60.81 ? C5 RET 306 B 1 HETATM 6 C C6 RET . . . P 5 -7.756 -29.09 20.886 1 58.08 ? C6 RET 306 B 1 HETATM 7 C C7 RET . . . P 5 -7.966 -30.402 20.239 1 57.84 ? C7 RET 306 B 1 HETATM 8 C C8 RET . . . P 5 -9.027 -30.622 19.469 1 50.55 ? C8 RET 306 B 1 HETATM 9 C C9 RET . . . P 5 -9.227 -31.925 18.81 1 54.7 ? C9 RET 306 B 1 HETATM 10 C C10 RET . . . P 5 -10.293 -32.059 18.017 1 57.27 ? C10 RET 306 B 1 HETATM 11 C C11 RET . . . P 5 -10.6 -33.289 17.287 1 59.4 ? C11 RET 306 B 1 HETATM 12 C C12 RET . . . P 5 -11.676 -33.24 16.507 1 64.46 ? C12 RET 306 B 1 HETATM 13 C C13 RET . . . P 5 -12.153 -34.349 15.66 1 57.02 ? C13 RET 306 B 1 HETATM 14 C C14 RET . . . P 5 -13.202 -34.067 14.877 1 56.07 ? C14 RET 306 B 1 HETATM 15 C C15 RET . . . P 5 -13.819 -35.064 13.935 1 55.06 ? C15 RET 306 B 1 HETATM 16 C C16 RET . . . P 5 -10.162 -28.526 21.102 1 59.95 ? C16 RET 306 B 1 HETATM 17 C C17 RET . . . P 5 -8.806 -27.596 19.226 1 58.34 ? C17 RET 306 B 1 HETATM 18 C C18 RET . . . P 5 -5.788 -30.104 21.953 1 68.16 ? C18 RET 306 B 1 HETATM 19 C C19 RET . . . P 5 -8.263 -33.056 19.019 1 67.17 ? C19 RET 306 B 1 HETATM 20 C C20 RET . . . P 5 -11.503 -35.702 15.649 1 54.01 ? C20 RET 306 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #