data_6RFA # _model_server_result.job_id faVhP6aLEaWppFFqfDSC-A _model_server_result.datetime_utc '2024-11-16 09:50:43' _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 6rfa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":337}' # _entry.id 6RFA # _exptl.entry_id 6RFA _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 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 6RFA _cell.length_a 40.738 _cell.length_b 84.178 _cell.length_c 234.541 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,JA,KA,LA,MA _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id LA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 LA C15 RET . A RET 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? metalc ? metalc1 A OH TYR 25 A TYR 25 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc2 A O THR 83 A THR 83 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc3 A O PHE 86 A PHE 86 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? # _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 338 n n C1 C6 RET sing 339 n n C1 C16 RET sing 340 n n C1 C17 RET sing 341 n n C2 C3 RET sing 342 n n C2 H21 RET sing 343 n n C2 H22 RET sing 344 n n C3 C4 RET sing 345 n n C3 H31 RET sing 346 n n C3 H32 RET sing 347 n n C4 C5 RET sing 348 n n C4 H41 RET sing 349 n n C4 H42 RET sing 350 n n C5 C6 RET doub 351 n n C5 C18 RET sing 352 n n C6 C7 RET sing 353 n n C7 C8 RET doub 354 e n C7 H7 RET sing 355 n n C8 C9 RET sing 356 n n C8 H8 RET sing 357 n n C9 C10 RET doub 358 e n C9 C19 RET sing 359 n n C10 C11 RET sing 360 n n C10 H10 RET sing 361 n n C11 C12 RET doub 362 e n C11 H11 RET sing 363 n n C12 C13 RET sing 364 n n C12 H12 RET sing 365 n n C13 C14 RET doub 366 e n C13 C20 RET sing 367 n n C14 C15 RET sing 368 n n C14 H14 RET sing 369 n n C15 O1 RET doub 370 n n C15 H15 RET sing 371 n n C16 H161 RET sing 372 n n C16 H162 RET sing 373 n n C16 H163 RET sing 374 n n C17 H171 RET sing 375 n n C17 H172 RET sing 376 n n C17 H173 RET sing 377 n n C18 H181 RET sing 378 n n C18 H182 RET sing 379 n n C18 H183 RET sing 380 n n C19 H191 RET sing 381 n n C19 H192 RET sing 382 n n C19 H193 RET sing 383 n n C20 H201 RET sing 384 n n C20 H202 RET sing 385 n n C20 H203 RET sing 386 n n # _atom_sites.entry_id 6RFA _atom_sites.fract_transf_matrix[1][1] 0.024547 _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] 0.01188 _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] 0.004264 _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 B 2 NA A 1 301 301 NA NA . C 3 LFA A 1 302 303 LFA LFA . D 3 LFA A 1 303 304 LFA LFA . E 3 LFA A 1 304 305 LFA LFA . F 3 LFA A 1 305 306 LFA LFA . G 3 LFA A 1 306 307 LFA LFA . H 3 LFA A 1 307 308 LFA LFA . I 3 LFA A 1 308 309 LFA LFA . J 3 LFA A 1 309 310 LFA LFA . K 3 LFA A 1 310 311 LFA LFA . L 3 LFA A 1 311 312 LFA LFA . M 3 LFA A 1 312 313 LFA LFA . N 3 LFA A 1 313 314 LFA LFA . O 3 LFA A 1 314 315 LFA LFA . P 3 LFA A 1 315 316 LFA LFA . Q 3 LFA A 1 316 317 LFA LFA . R 3 LFA A 1 317 318 LFA LFA . S 3 LFA A 1 318 319 LFA LFA . T 3 LFA A 1 319 320 LFA LFA . U 3 LFA A 1 320 321 LFA LFA . V 3 LFA A 1 321 322 LFA LFA . W 3 LFA A 1 322 323 LFA LFA . X 3 LFA A 1 323 324 LFA LFA . Y 3 LFA A 1 324 325 LFA LFA . Z 3 LFA A 1 325 326 LFA LFA . AA 3 LFA A 1 326 327 LFA LFA . BA 3 LFA A 1 327 328 LFA LFA . CA 3 LFA A 1 328 329 LFA LFA . DA 3 LFA A 1 329 330 LFA LFA . EA 3 LFA A 1 330 331 LFA LFA . FA 3 LFA A 1 331 332 LFA LFA . GA 3 LFA A 1 332 333 LFA LFA . HA 3 LFA A 1 333 334 LFA LFA . IA 3 LFA A 1 334 335 LFA LFA . JA 4 GOL A 1 335 336 GOL GOL . KA 3 LFA A 1 336 1 LFA LFA . LA 5 RET A 1 337 255 RET LYR . MA 6 HOH A 1 401 20 HOH HOH . MA 6 HOH A 2 402 14 HOH HOH . MA 6 HOH A 3 403 43 HOH HOH . MA 6 HOH A 4 404 31 HOH HOH . MA 6 HOH A 5 405 18 HOH HOH . MA 6 HOH A 6 406 12 HOH HOH . MA 6 HOH A 7 407 22 HOH HOH . MA 6 HOH A 8 408 40 HOH HOH . MA 6 HOH A 9 409 15 HOH HOH . MA 6 HOH A 10 410 26 HOH HOH . MA 6 HOH A 11 411 3 HOH HOH . MA 6 HOH A 12 412 11 HOH HOH . MA 6 HOH A 13 413 13 HOH HOH . MA 6 HOH A 14 414 6 HOH HOH . MA 6 HOH A 15 415 27 HOH HOH . MA 6 HOH A 16 416 8 HOH HOH . MA 6 HOH A 17 417 7 HOH HOH . MA 6 HOH A 18 418 17 HOH HOH . MA 6 HOH A 19 419 29 HOH HOH . MA 6 HOH A 20 420 42 HOH HOH . MA 6 HOH A 21 421 39 HOH HOH . MA 6 HOH A 22 422 9 HOH HOH . MA 6 HOH A 23 423 38 HOH HOH . MA 6 HOH A 24 424 16 HOH HOH . MA 6 HOH A 25 425 10 HOH HOH . MA 6 HOH A 26 426 5 HOH HOH . MA 6 HOH A 27 427 25 HOH HOH . MA 6 HOH A 28 428 21 HOH HOH . MA 6 HOH A 29 429 28 HOH HOH . MA 6 HOH A 30 430 37 HOH HOH . MA 6 HOH A 31 431 35 HOH HOH . MA 6 HOH A 32 432 36 HOH HOH . MA 6 HOH A 33 433 41 HOH HOH . MA 6 HOH A 34 434 34 HOH HOH . MA 6 HOH A 35 435 19 HOH HOH . MA 6 HOH A 36 436 30 HOH HOH . MA 6 HOH A 37 437 24 HOH HOH . MA 6 HOH A 38 438 23 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 . . . LA 5 -2.138 25.636 27.195 1 30.23 ? C1 RET 337 A 1 HETATM 2 C C2 RET . . . LA 5 -2.563 26.724 26.216 1 33.11 ? C2 RET 337 A 1 HETATM 3 C C3 RET . . . LA 5 -1.611 27.908 26.27 1 33.69 ? C3 RET 337 A 1 HETATM 4 C C4 RET . . . LA 5 -1.736 28.582 27.623 1 34.14 ? C4 RET 337 A 1 HETATM 5 C C5 RET . . . LA 5 -1.673 27.56 28.735 1 37.27 ? C5 RET 337 A 1 HETATM 6 C C6 RET . . . LA 5 -1.687 26.236 28.524 1 34.47 ? C6 RET 337 A 1 HETATM 7 C C7 RET . . . LA 5 -1.243 25.37 29.656 1 31.68 ? C7 RET 337 A 1 HETATM 8 C C8 RET . . . LA 5 -1.243 24.035 29.587 1 30.9 ? C8 RET 337 A 1 HETATM 9 C C9 RET . . . LA 5 -0.783 23.191 30.716 1 35.63 ? C9 RET 337 A 1 HETATM 10 C C10 RET . . . LA 5 -0.763 21.861 30.527 1 30.24 ? C10 RET 337 A 1 HETATM 11 C C11 RET . . . LA 5 -0.281 20.913 31.529 1 30.8 ? C11 RET 337 A 1 HETATM 12 C C12 RET . . . LA 5 -0.198 19.635 31.152 1 31.89 ? C12 RET 337 A 1 HETATM 13 C C13 RET . . . LA 5 0.312 18.555 32.017 1 30.06 ? C13 RET 337 A 1 HETATM 14 C C14 RET . . . LA 5 0.416 17.321 31.482 1 32.26 ? C14 RET 337 A 1 HETATM 15 C C15 RET . . . LA 5 0.949 16.137 32.255 1 30.08 ? C15 RET 337 A 1 HETATM 16 C C16 RET . . . LA 5 -3.302 24.681 27.438 1 27.1 ? C16 RET 337 A 1 HETATM 17 C C17 RET . . . LA 5 -0.985 24.878 26.548 1 31.29 ? C17 RET 337 A 1 HETATM 18 C C18 RET . . . LA 5 -1.586 28.072 30.142 1 35.42 ? C18 RET 337 A 1 HETATM 19 C C19 RET . . . LA 5 -0.349 23.797 32.027 1 34.19 ? C19 RET 337 A 1 HETATM 20 C C20 RET . . . LA 5 0.757 18.834 33.421 1 29.42 ? C20 RET 337 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #