data_5JJF # _model_server_result.job_id -W58pwsrMrV36twqAAB4jg _model_server_result.datetime_utc '2024-11-18 09:54:47' _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 5jjf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5JJF # _exptl.entry_id 5JJF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _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 5JJF _cell.length_a 49.558 _cell.length_b 113.779 _cell.length_c 125.387 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JJF _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_556 -x+1/2,y,-z+1 -1 0 0 0 1 0 0 0 -1 24.779 0 125.387 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 204 A LYS 205 1_555 C C15 RET . A RET 301 1_555 ? G ? ? G ? ? ? ? ? ? ? 1.318 ? covale ? covale2 A NZ LYS 204 A LYS 205 1_555 C C15 RET . A RET 301 1_555 ? M ? ? M ? ? ? ? ? ? ? 1.258 ? # _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 373 n n C1 C6 RET sing 374 n n C1 C16 RET sing 375 n n C1 C17 RET sing 376 n n C2 C3 RET sing 377 n n C2 H21 RET sing 378 n n C2 H22 RET sing 379 n n C3 C4 RET sing 380 n n C3 H31 RET sing 381 n n C3 H32 RET sing 382 n n C4 C5 RET sing 383 n n C4 H41 RET sing 384 n n C4 H42 RET sing 385 n n C5 C6 RET doub 386 n n C5 C18 RET sing 387 n n C6 C7 RET sing 388 n n C7 C8 RET doub 389 e n C7 H7 RET sing 390 n n C8 C9 RET sing 391 n n C8 H8 RET sing 392 n n C9 C10 RET doub 393 e n C9 C19 RET sing 394 n n C10 C11 RET sing 395 n n C10 H10 RET sing 396 n n C11 C12 RET doub 397 e n C11 H11 RET sing 398 n n C12 C13 RET sing 399 n n C12 H12 RET sing 400 n n C13 C14 RET doub 401 e n C13 C20 RET sing 402 n n C14 C15 RET sing 403 n n C14 H14 RET sing 404 n n C15 O1 RET doub 405 n n C15 H15 RET sing 406 n n C16 H161 RET sing 407 n n C16 H162 RET sing 408 n n C16 H163 RET sing 409 n n C17 H171 RET sing 410 n n C17 H172 RET sing 411 n n C17 H173 RET sing 412 n n C18 H181 RET sing 413 n n C18 H182 RET sing 414 n n C18 H183 RET sing 415 n n C19 H191 RET sing 416 n n C19 H192 RET sing 417 n n C19 H193 RET sing 418 n n C20 H201 RET sing 419 n n C20 H202 RET sing 420 n n C20 H203 RET sing 421 n n # _atom_sites.entry_id 5JJF _atom_sites.fract_transf_matrix[1][1] 0.020178 _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] 0.008789 _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] 0.007975 _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 C 3 RET A 1 301 301 RET RET . D 4 BOG A 1 302 1 BOG BOG . E 5 LFA A 1 303 2 LFA LFA . F 5 LFA A 1 304 3 LFA LFA . G 5 LFA A 1 305 4 LFA LFA . H 5 LFA A 1 306 5 LFA LFA . I 5 LFA A 1 307 7 LFA LFA . J 5 LFA A 1 308 8 LFA LFA . K 5 LFA A 1 309 9 LFA LFA . L 5 LFA A 1 310 1 LFA LFA . M 5 LFA A 1 311 1 LFA LFA . N 5 LFA B 1 201 1 LFA LFA . O 5 LFA B 1 202 6 LFA LFA . P 5 LFA B 1 203 1 LFA LFA . Q 6 HOH A 1 401 29 HOH HOH . Q 6 HOH A 2 402 33 HOH HOH . Q 6 HOH A 3 403 97 HOH HOH . Q 6 HOH A 4 404 30 HOH HOH . Q 6 HOH A 5 405 8 HOH HOH . Q 6 HOH A 6 406 13 HOH HOH . Q 6 HOH A 7 407 90 HOH HOH . Q 6 HOH A 8 408 19 HOH HOH . Q 6 HOH A 9 409 57 HOH HOH . Q 6 HOH A 10 410 95 HOH HOH . Q 6 HOH A 11 411 106 HOH HOH . Q 6 HOH A 12 412 51 HOH HOH . Q 6 HOH A 13 413 16 HOH HOH . Q 6 HOH A 14 414 68 HOH HOH . Q 6 HOH A 15 415 27 HOH HOH . Q 6 HOH A 16 416 88 HOH HOH . Q 6 HOH A 17 417 34 HOH HOH . Q 6 HOH A 18 418 38 HOH HOH . Q 6 HOH A 19 419 110 HOH HOH . Q 6 HOH A 20 420 7 HOH HOH . Q 6 HOH A 21 421 20 HOH HOH . Q 6 HOH A 22 422 54 HOH HOH . Q 6 HOH A 23 423 2 HOH HOH . Q 6 HOH A 24 424 65 HOH HOH . Q 6 HOH A 25 425 47 HOH HOH . Q 6 HOH A 26 426 22 HOH HOH . Q 6 HOH A 27 427 85 HOH HOH . Q 6 HOH A 28 428 104 HOH HOH . Q 6 HOH A 29 429 112 HOH HOH . Q 6 HOH A 30 430 25 HOH HOH . Q 6 HOH A 31 431 96 HOH HOH . Q 6 HOH A 32 432 82 HOH HOH . Q 6 HOH A 33 433 49 HOH HOH . Q 6 HOH A 34 434 91 HOH HOH . Q 6 HOH A 35 435 50 HOH HOH . Q 6 HOH A 36 436 107 HOH HOH . Q 6 HOH A 37 437 93 HOH HOH . Q 6 HOH A 38 438 59 HOH HOH . Q 6 HOH A 39 439 52 HOH HOH . Q 6 HOH A 40 440 99 HOH HOH . Q 6 HOH A 41 441 114 HOH HOH . Q 6 HOH A 42 442 111 HOH HOH . Q 6 HOH A 43 443 87 HOH HOH . Q 6 HOH A 44 444 117 HOH HOH . Q 6 HOH A 45 445 43 HOH HOH . Q 6 HOH A 46 446 92 HOH HOH . R 6 HOH B 1 301 17 HOH HOH . R 6 HOH B 2 302 109 HOH HOH . R 6 HOH B 3 303 28 HOH HOH . R 6 HOH B 4 304 103 HOH HOH . R 6 HOH B 5 305 94 HOH HOH . R 6 HOH B 6 306 102 HOH HOH . R 6 HOH B 7 307 55 HOH HOH . R 6 HOH B 8 308 115 HOH HOH . R 6 HOH B 9 309 84 HOH HOH . R 6 HOH B 10 310 113 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 . G . C 3 -6.688 5.385 51.221 0.5 23.38 ? C1 RET 301 A 1 HETATM 2 C C1 RET . M . C 3 -6.781 5.505 50.512 0.5 23.83 ? C1 RET 301 A 1 HETATM 3 C C2 RET . G . C 3 -7.419 6.528 51.87 0.5 23.82 ? C2 RET 301 A 1 HETATM 4 C C2 RET . M . C 3 -7.894 6.465 50.99 0.5 24.36 ? C2 RET 301 A 1 HETATM 5 C C3 RET . G . C 3 -8.782 5.979 52.226 0.5 23.77 ? C3 RET 301 A 1 HETATM 6 C C3 RET . M . C 3 -9.166 5.795 51.383 0.5 23.85 ? C3 RET 301 A 1 HETATM 7 C C4 RET . G . C 3 -8.517 4.871 53.272 0.5 24.48 ? C4 RET 301 A 1 HETATM 8 C C4 RET . M . C 3 -8.996 4.707 52.447 0.5 24.01 ? C4 RET 301 A 1 HETATM 9 C C5 RET . G . C 3 -7.561 3.724 53.008 0.5 23.16 ? C5 RET 301 A 1 HETATM 10 C C5 RET . M . C 3 -7.712 3.862 52.311 0.5 22.9 ? C5 RET 301 A 1 HETATM 11 C C6 RET . G . C 3 -6.736 4.009 51.96 0.5 22.39 ? C6 RET 301 A 1 HETATM 12 C C6 RET . M . C 3 -6.834 4.104 51.241 0.5 23.13 ? C6 RET 301 A 1 HETATM 13 C C7 RET . G . C 3 -5.828 2.897 51.61 0.5 22.39 ? C7 RET 301 A 1 HETATM 14 C C7 RET . M . C 3 -5.796 3.045 51.022 0.5 22.81 ? C7 RET 301 A 1 HETATM 15 C C8 RET . G . C 3 -4.867 2.908 50.622 0.5 22.61 ? C8 RET 301 A 1 HETATM 16 C C8 RET . M . C 3 -4.932 2.825 49.971 0.5 23.24 ? C8 RET 301 A 1 HETATM 17 C C9 RET . G . C 3 -3.99 1.809 50.227 0.5 23.73 ? C9 RET 301 A 1 HETATM 18 C C9 RET . M . C 3 -4.032 1.671 49.782 0.5 24.29 ? C9 RET 301 A 1 HETATM 19 C C10 RET . G . C 3 -3.11 2.029 49.197 0.5 24.8 ? C10 RET 301 A 1 HETATM 20 C C10 RET . M . C 3 -3.143 1.833 48.739 0.5 24.85 ? C10 RET 301 A 1 HETATM 21 C C11 RET . G . C 3 -2.195 0.925 48.792 0.5 25.13 ? C11 RET 301 A 1 HETATM 22 C C11 RET . M . C 3 -2.39 0.673 48.186 0.5 25.03 ? C11 RET 301 A 1 HETATM 23 C C12 RET . G . C 3 -1.482 1.256 47.659 0.5 25.79 ? C12 RET 301 A 1 HETATM 24 C C12 RET . M . C 3 -1.49 1.024 47.199 0.5 26.04 ? C12 RET 301 A 1 HETATM 25 C C13 RET . G . C 3 -0.471 0.346 47.089 0.5 26.31 ? C13 RET 301 A 1 HETATM 26 C C13 RET . M . C 3 -0.634 0.018 46.559 0.5 26.27 ? C13 RET 301 A 1 HETATM 27 C C14 RET . G . C 3 0.159 0.823 45.98 0.5 26.55 ? C14 RET 301 A 1 HETATM 28 C C14 RET . M . C 3 0.132 -0.064 45.438 0.5 27.33 ? C14 RET 301 A 1 HETATM 29 C C15 RET . G . C 3 1.086 0.029 45.175 0.5 27.38 ? C15 RET 301 A 1 HETATM 30 C C15 RET . M . C 3 0.698 0.868 44.487 0.5 29.59 ? C15 RET 301 A 1 HETATM 31 C C16 RET . G . C 3 -7.187 5.179 49.732 0.5 22.93 ? C16 RET 301 A 1 HETATM 32 C C16 RET . M . C 3 -6.95 5.332 48.94 0.5 22.35 ? C16 RET 301 A 1 HETATM 33 C C17 RET . G . C 3 -5.214 6.03 51.141 0.5 25.16 ? C17 RET 301 A 1 HETATM 34 C C17 RET . M . C 3 -5.454 6.329 50.857 0.5 26 ? C17 RET 301 A 1 HETATM 35 C C18 RET . G . C 3 -7.67 2.485 53.831 0.5 23.65 ? C18 RET 301 A 1 HETATM 36 C C18 RET . M . C 3 -7.805 2.664 53.239 0.5 23.67 ? C18 RET 301 A 1 HETATM 37 C C19 RET . G . C 3 -4.036 0.566 51.043 0.5 23.66 ? C19 RET 301 A 1 HETATM 38 C C19 RET . M . C 3 -4.085 0.471 50.679 0.5 23.75 ? C19 RET 301 A 1 HETATM 39 C C20 RET . G . C 3 -0.349 -1.056 47.618 0.5 25.52 ? C20 RET 301 A 1 HETATM 40 C C20 RET . M . C 3 -0.39 -1.369 47.047 0.5 26.11 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #