data_6RFC # _model_server_result.job_id myb5kJlR0MhJSVWGrL2crA _model_server_result.datetime_utc '2024-11-16 08:49:19' _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 6rfc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":337}' # _entry.id 6RFC # _exptl.entry_id 6RFC _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 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 6RFC _cell.length_a 40.769 _cell.length_b 81.964 _cell.length_c 232.93 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RFC _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 6 _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OH TYR 25 A TYR 25 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc2 A O THR 83 A THR 83 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 A O PHE 86 A PHE 86 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc4 B NA NA . A NA 301 1_555 MA O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc5 B NA NA . A NA 301 1_555 MA O HOH . A HOH 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc6 B NA NA . A NA 301 1_555 MA O HOH . A HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? # _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 402 n n C1 C6 RET sing 403 n n C1 C16 RET sing 404 n n C1 C17 RET sing 405 n n C2 C3 RET sing 406 n n C2 H21 RET sing 407 n n C2 H22 RET sing 408 n n C3 C4 RET sing 409 n n C3 H31 RET sing 410 n n C3 H32 RET sing 411 n n C4 C5 RET sing 412 n n C4 H41 RET sing 413 n n C4 H42 RET sing 414 n n C5 C6 RET doub 415 n n C5 C18 RET sing 416 n n C6 C7 RET sing 417 n n C7 C8 RET doub 418 e n C7 H7 RET sing 419 n n C8 C9 RET sing 420 n n C8 H8 RET sing 421 n n C9 C10 RET doub 422 e n C9 C19 RET sing 423 n n C10 C11 RET sing 424 n n C10 H10 RET sing 425 n n C11 C12 RET doub 426 e n C11 H11 RET sing 427 n n C12 C13 RET sing 428 n n C12 H12 RET sing 429 n n C13 C14 RET doub 430 e n C13 C20 RET sing 431 n n C14 C15 RET sing 432 n n C14 H14 RET sing 433 n n C15 O1 RET doub 434 n n C15 H15 RET sing 435 n n C16 H161 RET sing 436 n n C16 H162 RET sing 437 n n C16 H163 RET sing 438 n n C17 H171 RET sing 439 n n C17 H172 RET sing 440 n n C17 H173 RET sing 441 n n C18 H181 RET sing 442 n n C18 H182 RET sing 443 n n C18 H183 RET sing 444 n n C19 H191 RET sing 445 n n C19 H192 RET sing 446 n n C19 H193 RET sing 447 n n C20 H201 RET sing 448 n n C20 H202 RET sing 449 n n C20 H203 RET sing 450 n n # _atom_sites.entry_id 6RFC _atom_sites.fract_transf_matrix[1][1] 0.024528 _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] 0.0122 _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] 0.004293 _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 1 302 302 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 1 307 309 LFA LFA . I 3 LFA A 1 308 310 LFA LFA . J 3 LFA A 1 309 311 LFA LFA . K 3 LFA A 1 310 314 LFA LFA . L 3 LFA A 1 311 315 LFA LFA . M 3 LFA A 1 312 316 LFA LFA . N 3 LFA A 1 313 317 LFA LFA . O 3 LFA A 1 314 318 LFA LFA . P 3 LFA A 1 315 319 LFA LFA . Q 3 LFA A 1 316 320 LFA LFA . R 3 LFA A 1 317 321 LFA LFA . S 3 LFA A 1 318 322 LFA LFA . T 3 LFA A 1 319 325 LFA LFA . U 3 LFA A 1 320 326 LFA LFA . V 3 LFA A 1 321 327 LFA LFA . W 3 LFA A 1 322 329 LFA LFA . X 3 LFA A 1 323 330 LFA LFA . Y 3 LFA A 1 324 331 LFA LFA . Z 3 LFA A 1 325 332 LFA LFA . AA 3 LFA A 1 326 333 LFA LFA . BA 3 LFA A 1 327 334 LFA LFA . CA 4 OLC A 1 328 1 OLC OLC . DA 4 OLC A 1 329 2 OLC OLC . EA 4 OLC A 1 330 3 OLC OLC . FA 5 GOL A 1 331 1 GOL GOL . GA 5 GOL A 1 332 2 GOL GOL . HA 5 GOL A 1 333 3 GOL GOL . IA 3 LFA A 1 334 1 LFA LFA . JA 3 LFA A 1 335 2 LFA LFA . KA 3 LFA A 1 336 3 LFA LFA . LA 6 RET A 1 337 255 RET LYR . MA 7 HOH A 1 401 41 HOH HOH . MA 7 HOH A 2 402 42 HOH HOH . MA 7 HOH A 3 403 3 HOH HOH . MA 7 HOH A 4 404 9 HOH HOH . MA 7 HOH A 5 405 50 HOH HOH . MA 7 HOH A 6 406 29 HOH HOH . MA 7 HOH A 7 407 16 HOH HOH . MA 7 HOH A 8 408 18 HOH HOH . MA 7 HOH A 9 409 47 HOH HOH . MA 7 HOH A 10 410 13 HOH HOH . MA 7 HOH A 11 411 27 HOH HOH . MA 7 HOH A 12 412 52 HOH HOH . MA 7 HOH A 13 413 4 HOH HOH . MA 7 HOH A 14 414 37 HOH HOH . MA 7 HOH A 15 415 1 HOH HOH . MA 7 HOH A 16 416 43 HOH HOH . MA 7 HOH A 17 417 28 HOH HOH . MA 7 HOH A 18 418 38 HOH HOH . MA 7 HOH A 19 419 23 HOH HOH . MA 7 HOH A 20 420 30 HOH HOH . MA 7 HOH A 21 421 15 HOH HOH . MA 7 HOH A 22 422 51 HOH HOH . MA 7 HOH A 23 423 55 HOH HOH . MA 7 HOH A 24 424 33 HOH HOH . MA 7 HOH A 25 425 35 HOH HOH . MA 7 HOH A 26 426 46 HOH HOH . MA 7 HOH A 27 427 25 HOH HOH . MA 7 HOH A 28 428 40 HOH HOH . MA 7 HOH A 29 429 2 HOH HOH . MA 7 HOH A 30 430 44 HOH HOH . MA 7 HOH A 31 431 11 HOH HOH . MA 7 HOH A 32 432 5 HOH HOH . MA 7 HOH A 33 433 14 HOH HOH . MA 7 HOH A 34 434 31 HOH HOH . MA 7 HOH A 35 435 22 HOH HOH . MA 7 HOH A 36 436 7 HOH HOH . MA 7 HOH A 37 437 26 HOH HOH . MA 7 HOH A 38 438 19 HOH HOH . MA 7 HOH A 39 439 34 HOH HOH . MA 7 HOH A 40 440 8 HOH HOH . MA 7 HOH A 41 441 10 HOH HOH . MA 7 HOH A 42 442 6 HOH HOH . MA 7 HOH A 43 443 17 HOH HOH . MA 7 HOH A 44 444 39 HOH HOH . MA 7 HOH A 45 445 32 HOH HOH . MA 7 HOH A 46 446 45 HOH HOH . MA 7 HOH A 47 447 12 HOH HOH . MA 7 HOH A 48 448 21 HOH HOH . MA 7 HOH A 49 449 20 HOH HOH . MA 7 HOH A 50 450 53 HOH HOH . MA 7 HOH A 51 451 54 HOH HOH . MA 7 HOH A 52 452 24 HOH HOH . MA 7 HOH A 53 453 49 HOH HOH . MA 7 HOH A 54 454 48 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 6 2.513 15.454 27.096 1 33.5 ? C1 RET 337 A 1 HETATM 2 C C2 RET . . . LA 6 3.097 14.4 26.16 1 41.16 ? C2 RET 337 A 1 HETATM 3 C C3 RET . . . LA 6 2.253 13.144 26.143 1 33.85 ? C3 RET 337 A 1 HETATM 4 C C4 RET . . . LA 6 2.287 12.5 27.515 1 37.94 ? C4 RET 337 A 1 HETATM 5 C C5 RET . . . LA 6 2.038 13.509 28.608 1 34.87 ? C5 RET 337 A 1 HETATM 6 C C6 RET . . . LA 6 2.052 14.841 28.417 1 29.66 ? C6 RET 337 A 1 HETATM 7 C C7 RET . . . LA 6 1.571 15.694 29.528 1 27.79 ? C7 RET 337 A 1 HETATM 8 C C8 RET . . . LA 6 1.503 17.035 29.427 1 29.48 ? C8 RET 337 A 1 HETATM 9 C C9 RET . . . LA 6 0.985 17.872 30.54 1 33.07 ? C9 RET 337 A 1 HETATM 10 C C10 RET . . . LA 6 0.943 19.208 30.371 1 25.42 ? C10 RET 337 A 1 HETATM 11 C C11 RET . . . LA 6 0.423 20.124 31.376 1 26.54 ? C11 RET 337 A 1 HETATM 12 C C12 RET . . . LA 6 0.36 21.397 30.972 1 25.99 ? C12 RET 337 A 1 HETATM 13 C C13 RET . . . LA 6 -0.173 22.472 31.798 1 30.45 ? C13 RET 337 A 1 HETATM 14 C C14 RET . . . LA 6 -0.264 23.681 31.222 1 31.27 ? C14 RET 337 A 1 HETATM 15 C C15 RET . . . LA 6 -0.817 24.856 31.949 1 30.61 ? C15 RET 337 A 1 HETATM 16 C C16 RET . . . LA 6 3.627 16.455 27.333 1 32.49 ? C16 RET 337 A 1 HETATM 17 C C17 RET . . . LA 6 1.342 16.142 26.402 1 34.17 ? C17 RET 337 A 1 HETATM 18 C C18 RET . . . LA 6 1.759 12.942 29.968 1 33.52 ? C18 RET 337 A 1 HETATM 19 C C19 RET . . . LA 6 0.504 17.253 31.819 1 27.91 ? C19 RET 337 A 1 HETATM 20 C C20 RET . . . LA 6 -0.623 22.209 33.2 1 27.44 ? C20 RET 337 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #