data_5JJN # _model_server_result.job_id Ux87PE1psfaisUIYaPlcCA _model_server_result.datetime_utc '2024-11-14 23:40:45' _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 5jjn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":307}' # _entry.id 5JJN # _exptl.entry_id 5JJN _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 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 5JJN _cell.length_a 47.131 _cell.length_b 109.096 _cell.length_c 121.818 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JJN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,S,T,U,V,W,X,Y,Z,AA _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 N N N ? 5 V 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 204 A LYS 205 1_555 N C15 RET . A RET 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale2 C NZ LYS 204 C LYS 205 1_555 V C15 RET . C RET 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? # _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 5JJN _atom_sites.fract_transf_matrix[1][1] 0.021217 _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] 0.009166 _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] 0.008209 _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 E 3 LFA A 1 301 302 LFA LFA . F 3 LFA A 1 302 303 LFA LFA . G 3 LFA A 1 303 304 LFA LFA . H 3 LFA A 1 304 305 LFA LFA . I 3 LFA A 1 305 306 LFA LFA . J 3 LFA A 1 306 307 LFA LFA . K 3 LFA A 1 307 308 LFA LFA . L 3 LFA A 1 308 309 LFA LFA . M 4 BOG A 1 309 310 BOG BOG . N 5 RET A 1 310 311 RET RET . O 3 LFA A 1 311 303 LFA LFA . P 3 LFA C 1 301 301 LFA LFA . Q 3 LFA C 1 302 301 LFA LFA . R 3 LFA C 1 303 302 LFA LFA . S 3 LFA C 1 304 304 LFA LFA . T 4 BOG C 1 305 305 BOG BOG . U 3 LFA C 1 306 306 LFA LFA . V 5 RET C 1 307 307 RET RET . W 3 LFA D 1 201 201 LFA LFA . X 6 HOH A 1 401 415 HOH HOH . X 6 HOH A 2 402 447 HOH HOH . X 6 HOH A 3 403 409 HOH HOH . X 6 HOH A 4 404 430 HOH HOH . X 6 HOH A 5 405 418 HOH HOH . X 6 HOH A 6 406 403 HOH HOH . X 6 HOH A 7 407 417 HOH HOH . X 6 HOH A 8 408 408 HOH HOH . X 6 HOH A 9 409 440 HOH HOH . X 6 HOH A 10 410 405 HOH HOH . X 6 HOH A 11 411 414 HOH HOH . X 6 HOH A 12 412 404 HOH HOH . X 6 HOH A 13 413 421 HOH HOH . X 6 HOH A 14 414 401 HOH HOH . X 6 HOH A 15 415 445 HOH HOH . X 6 HOH A 16 416 437 HOH HOH . X 6 HOH A 17 417 406 HOH HOH . X 6 HOH A 18 418 419 HOH HOH . X 6 HOH A 19 419 416 HOH HOH . X 6 HOH A 20 420 410 HOH HOH . X 6 HOH A 21 421 413 HOH HOH . X 6 HOH A 22 422 428 HOH HOH . X 6 HOH A 23 423 411 HOH HOH . X 6 HOH A 24 424 412 HOH HOH . X 6 HOH A 25 425 434 HOH HOH . X 6 HOH A 26 426 429 HOH HOH . X 6 HOH A 27 427 425 HOH HOH . X 6 HOH A 28 428 441 HOH HOH . X 6 HOH A 29 429 423 HOH HOH . X 6 HOH A 30 430 427 HOH HOH . X 6 HOH A 31 431 435 HOH HOH . X 6 HOH A 32 432 402 HOH HOH . X 6 HOH A 33 433 436 HOH HOH . X 6 HOH A 34 434 407 HOH HOH . X 6 HOH A 35 435 422 HOH HOH . X 6 HOH A 36 436 420 HOH HOH . X 6 HOH A 37 437 442 HOH HOH . X 6 HOH A 38 438 426 HOH HOH . X 6 HOH A 39 439 432 HOH HOH . X 6 HOH A 40 440 433 HOH HOH . X 6 HOH A 41 441 423 HOH HOH . X 6 HOH A 42 442 424 HOH HOH . X 6 HOH A 43 443 431 HOH HOH . X 6 HOH A 44 444 438 HOH HOH . X 6 HOH A 45 445 446 HOH HOH . X 6 HOH A 46 446 439 HOH HOH . X 6 HOH A 47 447 444 HOH HOH . X 6 HOH A 48 448 443 HOH HOH . Y 6 HOH B 1 201 202 HOH HOH . Y 6 HOH B 2 202 201 HOH HOH . Y 6 HOH B 3 203 203 HOH HOH . Z 6 HOH C 1 401 440 HOH HOH . Z 6 HOH C 2 402 408 HOH HOH . Z 6 HOH C 3 403 427 HOH HOH . Z 6 HOH C 4 404 416 HOH HOH . Z 6 HOH C 5 405 405 HOH HOH . Z 6 HOH C 6 406 437 HOH HOH . Z 6 HOH C 7 407 411 HOH HOH . Z 6 HOH C 8 408 426 HOH HOH . Z 6 HOH C 9 409 407 HOH HOH . Z 6 HOH C 10 410 406 HOH HOH . Z 6 HOH C 11 411 409 HOH HOH . Z 6 HOH C 12 412 424 HOH HOH . Z 6 HOH C 13 413 414 HOH HOH . Z 6 HOH C 14 414 417 HOH HOH . Z 6 HOH C 15 415 419 HOH HOH . Z 6 HOH C 16 416 413 HOH HOH . Z 6 HOH C 17 417 415 HOH HOH . Z 6 HOH C 18 418 401 HOH HOH . Z 6 HOH C 19 419 435 HOH HOH . Z 6 HOH C 20 420 439 HOH HOH . Z 6 HOH C 21 421 403 HOH HOH . Z 6 HOH C 22 422 430 HOH HOH . Z 6 HOH C 23 423 420 HOH HOH . Z 6 HOH C 24 424 425 HOH HOH . Z 6 HOH C 25 425 418 HOH HOH . Z 6 HOH C 26 426 402 HOH HOH . Z 6 HOH C 27 427 441 HOH HOH . Z 6 HOH C 28 428 412 HOH HOH . Z 6 HOH C 29 429 432 HOH HOH . Z 6 HOH C 30 430 433 HOH HOH . Z 6 HOH C 31 431 404 HOH HOH . Z 6 HOH C 32 432 429 HOH HOH . Z 6 HOH C 33 433 410 HOH HOH . Z 6 HOH C 34 434 434 HOH HOH . Z 6 HOH C 35 435 438 HOH HOH . Z 6 HOH C 36 436 422 HOH HOH . Z 6 HOH C 37 437 431 HOH HOH . Z 6 HOH C 38 438 421 HOH HOH . Z 6 HOH C 39 439 428 HOH HOH . Z 6 HOH C 40 440 436 HOH HOH . AA 6 HOH D 1 301 302 HOH HOH . AA 6 HOH D 2 302 301 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 . . . V 5 70.886 -1.265 50.738 1 27.82 ? C1 RET 307 C 1 HETATM 2 C C2 RET . . . V 5 69.909 -2.488 50.874 1 25.53 ? C2 RET 307 C 1 HETATM 3 C C3 RET . . . V 5 68.895 -1.975 51.863 1 25.49 ? C3 RET 307 C 1 HETATM 4 C C4 RET . . . V 5 68.347 -0.764 50.985 1 26.35 ? C4 RET 307 C 1 HETATM 5 C C5 RET . . . V 5 69.118 0.267 50.516 1 29.01 ? C5 RET 307 C 1 HETATM 6 C C6 RET . . . V 5 70.451 0.016 50.314 1 20.05 ? C6 RET 307 C 1 HETATM 7 C C7 RET . . . V 5 71.192 1.117 49.853 1 12.95 ? C7 RET 307 C 1 HETATM 8 C C8 RET . . . V 5 72.672 0.971 49.604 1 14.59 ? C8 RET 307 C 1 HETATM 9 C C9 RET . . . V 5 73.46 2.154 49.115 1 23.13 ? C9 RET 307 C 1 HETATM 10 C C10 RET . . . V 5 74.924 1.883 48.91 1 18.94 ? C10 RET 307 C 1 HETATM 11 C C11 RET . . . V 5 75.778 3.013 48.426 1 25.44 ? C11 RET 307 C 1 HETATM 12 C C12 RET . . . V 5 77.181 2.5 48.304 1 19.93 ? C12 RET 307 C 1 HETATM 13 C C13 RET . . . V 5 78.216 3.474 47.837 1 23.98 ? C13 RET 307 C 1 HETATM 14 C C14 RET . . . V 5 79.629 2.937 47.721 1 25.85 ? C14 RET 307 C 1 HETATM 15 C C15 RET . . . V 5 80.677 3.907 47.26 1 34.21 ? C15 RET 307 C 1 HETATM 16 C C16 RET . . . V 5 71.855 -1.212 51.924 1 28.82 ? C16 RET 307 C 1 HETATM 17 C C17 RET . . . V 5 71.647 -1.914 49.559 1 24.67 ? C17 RET 307 C 1 HETATM 18 C C18 RET . . . V 5 68.576 1.523 50.266 1 26.84 ? C18 RET 307 C 1 HETATM 19 C C19 RET . . . V 5 72.817 3.501 48.773 1 19.46 ? C19 RET 307 C 1 HETATM 20 C C20 RET . . . V 5 77.829 4.897 47.414 1 23.5 ? C20 RET 307 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #