data_4JQ6 # _model_server_result.job_id bprMuCj69kWR-i7CghIWdg _model_server_result.datetime_utc '2025-01-10 11:09:25' _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 4jq6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 4JQ6 # _exptl.entry_id 4JQ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 119.52 _cell.angle_gamma 90 _cell.entry_id 4JQ6 _cell.length_a 87.267 _cell.length_b 101.952 _cell.length_c 87.357 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JQ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 H 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 213 A LYS 213 1_555 D C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale2 B NZ LYS 213 B LYS 213 1_555 E C15 RET . B RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale3 C NZ LYS 213 C LYS 213 1_555 H C15 RET . C RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? # _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 394 n n C1 C6 RET sing 395 n n C1 C16 RET sing 396 n n C1 C17 RET sing 397 n n C2 C3 RET sing 398 n n C2 H21 RET sing 399 n n C2 H22 RET sing 400 n n C3 C4 RET sing 401 n n C3 H31 RET sing 402 n n C3 H32 RET sing 403 n n C4 C5 RET sing 404 n n C4 H41 RET sing 405 n n C4 H42 RET sing 406 n n C5 C6 RET doub 407 n n C5 C18 RET sing 408 n n C6 C7 RET sing 409 n n C7 C8 RET doub 410 e n C7 H7 RET sing 411 n n C8 C9 RET sing 412 n n C8 H8 RET sing 413 n n C9 C10 RET doub 414 e n C9 C19 RET sing 415 n n C10 C11 RET sing 416 n n C10 H10 RET sing 417 n n C11 C12 RET doub 418 e n C11 H11 RET sing 419 n n C12 C13 RET sing 420 n n C12 H12 RET sing 421 n n C13 C14 RET doub 422 e n C13 C20 RET sing 423 n n C14 C15 RET sing 424 n n C14 H14 RET sing 425 n n C15 O1 RET doub 426 n n C15 H15 RET sing 427 n n C16 H161 RET sing 428 n n C16 H162 RET sing 429 n n C16 H163 RET sing 430 n n C17 H171 RET sing 431 n n C17 H172 RET sing 432 n n C17 H173 RET sing 433 n n C18 H181 RET sing 434 n n C18 H182 RET sing 435 n n C18 H183 RET sing 436 n n C19 H191 RET sing 437 n n C19 H192 RET sing 438 n n C19 H193 RET sing 439 n n C20 H201 RET sing 440 n n C20 H202 RET sing 441 n n C20 H203 RET sing 442 n n # _atom_sites.entry_id 4JQ6 _atom_sites.fract_transf_matrix[1][1] 0.011459 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006489 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009809 _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] 0.013155 _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 D 2 RET A 1 301 301 RET RET . E 2 RET B 1 301 301 RET RET . F 3 LI1 B 1 302 1 LI1 LI1 . G 3 LI1 B 1 303 2 LI1 LI1 . H 2 RET C 1 301 301 RET RET . I 4 HOH A 1 403 403 HOH HOH . I 4 HOH A 2 405 405 HOH HOH . I 4 HOH A 3 410 410 HOH HOH . I 4 HOH A 4 503 503 HOH HOH . I 4 HOH A 5 504 504 HOH HOH . I 4 HOH A 6 1001 7 HOH HOH . I 4 HOH A 7 1002 10 HOH HOH . I 4 HOH A 8 1003 11 HOH HOH . I 4 HOH A 9 1004 13 HOH HOH . I 4 HOH A 10 1005 14 HOH HOH . I 4 HOH A 11 1006 32 HOH HOH . J 4 HOH B 1 403 403 HOH HOH . J 4 HOH B 2 405 405 HOH HOH . J 4 HOH B 3 410 410 HOH HOH . J 4 HOH B 4 501 501 HOH HOH . J 4 HOH B 5 502 502 HOH HOH . J 4 HOH B 6 1001 1 HOH HOH . J 4 HOH B 7 1002 2 HOH HOH . J 4 HOH B 8 1003 8 HOH HOH . J 4 HOH B 9 1004 18 HOH HOH . J 4 HOH B 10 1005 19 HOH HOH . J 4 HOH B 11 1006 20 HOH HOH . J 4 HOH B 12 1007 25 HOH HOH . J 4 HOH B 13 1008 26 HOH HOH . J 4 HOH B 14 1009 27 HOH HOH . J 4 HOH B 15 1010 28 HOH HOH . J 4 HOH B 16 1011 29 HOH HOH . J 4 HOH B 17 1012 30 HOH HOH . J 4 HOH B 18 1013 31 HOH HOH . J 4 HOH B 19 1014 22 HOH HOH . K 4 HOH C 1 403 403 HOH HOH . K 4 HOH C 2 405 405 HOH HOH . K 4 HOH C 3 410 410 HOH HOH . K 4 HOH C 4 1001 3 HOH HOH . K 4 HOH C 5 1002 4 HOH HOH . K 4 HOH C 6 1003 5 HOH HOH . K 4 HOH C 7 1004 6 HOH HOH . K 4 HOH C 8 1005 9 HOH HOH . K 4 HOH C 9 1006 15 HOH HOH . K 4 HOH C 10 1007 16 HOH HOH . K 4 HOH C 11 1008 17 HOH HOH . K 4 HOH C 12 1009 21 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 . . . E 2 29.797 -2.2 -21.421 1 37 ? C1 RET 301 B 1 HETATM 2 C C2 RET . . . E 2 29.971 -3.304 -22.456 1 37.21 ? C2 RET 301 B 1 HETATM 3 C C3 RET . . . E 2 30.599 -2.784 -23.763 1 38.42 ? C3 RET 301 B 1 HETATM 4 C C4 RET . . . E 2 31.604 -1.656 -23.547 1 35.95 ? C4 RET 301 B 1 HETATM 5 C C5 RET . . . E 2 30.941 -0.515 -22.818 1 37.35 ? C5 RET 301 B 1 HETATM 6 C C6 RET . . . E 2 30.033 -0.736 -21.84 1 37.18 ? C6 RET 301 B 1 HETATM 7 C C7 RET . . . E 2 29.395 0.476 -21.208 1 36.1 ? C7 RET 301 B 1 HETATM 8 C C8 RET . . . E 2 28.476 0.484 -20.233 1 36.61 ? C8 RET 301 B 1 HETATM 9 C C9 RET . . . E 2 27.854 1.694 -19.621 1 38.21 ? C9 RET 301 B 1 HETATM 10 C C10 RET . . . E 2 26.94 1.5 -18.644 1 39.42 ? C10 RET 301 B 1 HETATM 11 C C11 RET . . . E 2 26.227 2.568 -17.936 1 39 ? C11 RET 301 B 1 HETATM 12 C C12 RET . . . E 2 25.366 2.211 -16.985 1 40.77 ? C12 RET 301 B 1 HETATM 13 C C13 RET . . . E 2 24.55 3.139 -16.158 1 43.05 ? C13 RET 301 B 1 HETATM 14 C C14 RET . . . E 2 23.73 2.569 -15.254 1 43.25 ? C14 RET 301 B 1 HETATM 15 C C15 RET . . . E 2 22.838 3.291 -14.341 1 44.42 ? C15 RET 301 B 1 HETATM 16 C C16 RET . . . E 2 29.278 -2.346 -19.99 1 37.49 ? C16 RET 301 B 1 HETATM 17 C C17 RET . . . E 2 28.325 -2.292 -21.854 1 36.7 ? C17 RET 301 B 1 HETATM 18 C C18 RET . . . E 2 31.31 0.869 -23.251 1 36.94 ? C18 RET 301 B 1 HETATM 19 C C19 RET . . . E 2 28.199 3.092 -20.051 1 37.08 ? C19 RET 301 B 1 HETATM 20 C C20 RET . . . E 2 24.631 4.638 -16.322 1 42.97 ? C20 RET 301 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #