data_4YZI # _model_server_result.job_id 3_ubCTIjB68mubRlHmLh_Q _model_server_result.datetime_utc '2025-02-23 03:34:36' _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 4yzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4YZI # _exptl.entry_id 4YZI _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 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 4YZI _cell.length_a 59.64 _cell.length_b 142.42 _cell.length_c 92.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YZI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -46.12 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 28 A CYS 66 1_555 A SG CYS 28 A CYS 66 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 A SG CYS 35 A CYS 73 1_555 A SG CYS 37 A CYS 75 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A NZ LYS 258 A LYS 296 1_555 B C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? metalc ? metalc1 A OD1 ASP 2 A ASP 40 1_555 H ZN ZN . A ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc2 A ND1 HIS 6 A HIS 44 1_555 H ZN ZN . A ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc3 A NE2 HIS 9 A HIS 47 1_555 H ZN ZN . A ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc4 A OD1 ASP 104 A ASP 142 1_555 H ZN ZN . A ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? # _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 330 n n C1 C6 RET sing 331 n n C1 C16 RET sing 332 n n C1 C17 RET sing 333 n n C2 C3 RET sing 334 n n C2 H21 RET sing 335 n n C2 H22 RET sing 336 n n C3 C4 RET sing 337 n n C3 H31 RET sing 338 n n C3 H32 RET sing 339 n n C4 C5 RET sing 340 n n C4 H41 RET sing 341 n n C4 H42 RET sing 342 n n C5 C6 RET doub 343 n n C5 C18 RET sing 344 n n C6 C7 RET sing 345 n n C7 C8 RET doub 346 e n C7 H7 RET sing 347 n n C8 C9 RET sing 348 n n C8 H8 RET sing 349 n n C9 C10 RET doub 350 e n C9 C19 RET sing 351 n n C10 C11 RET sing 352 n n C10 H10 RET sing 353 n n C11 C12 RET doub 354 e n C11 H11 RET sing 355 n n C12 C13 RET sing 356 n n C12 H12 RET sing 357 n n C13 C14 RET doub 358 e n C13 C20 RET sing 359 n n C14 C15 RET sing 360 n n C14 H14 RET sing 361 n n C15 O1 RET doub 362 n n C15 H15 RET sing 363 n n C16 H161 RET sing 364 n n C16 H162 RET sing 365 n n C16 H163 RET sing 366 n n C17 H171 RET sing 367 n n C17 H172 RET sing 368 n n C17 H173 RET sing 369 n n C18 H181 RET sing 370 n n C18 H182 RET sing 371 n n C18 H183 RET sing 372 n n C19 H191 RET sing 373 n n C19 H192 RET sing 374 n n C19 H193 RET sing 375 n n C20 H201 RET sing 376 n n C20 H202 RET sing 377 n n C20 H203 RET sing 378 n n # _atom_sites.entry_id 4YZI _atom_sites.fract_transf_matrix[1][1] 0.016767 _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] 0.007021 _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] 0.010841 _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 RET A 1 401 1 RET RET . C 3 OLA A 1 402 1 OLA OLA . D 3 OLA A 1 403 2 OLA OLA . E 3 OLA A 1 404 3 OLA OLA . F 3 OLA A 1 405 4 OLA OLA . G 3 OLA A 1 406 5 OLA OLA . H 4 ZN A 1 407 1 ZN ZN . I 5 HOH A 1 501 16 HOH HOH . I 5 HOH A 2 502 13 HOH HOH . I 5 HOH A 3 503 2 HOH HOH . I 5 HOH A 4 504 9 HOH HOH . I 5 HOH A 5 505 3 HOH HOH . I 5 HOH A 6 506 15 HOH HOH . I 5 HOH A 7 507 19 HOH HOH . I 5 HOH A 8 508 8 HOH HOH . I 5 HOH A 9 509 4 HOH HOH . I 5 HOH A 10 510 1 HOH HOH . I 5 HOH A 11 511 14 HOH HOH . I 5 HOH A 12 512 10 HOH HOH . I 5 HOH A 13 513 6 HOH HOH . I 5 HOH A 14 514 17 HOH HOH . I 5 HOH A 15 515 5 HOH HOH . I 5 HOH A 16 516 12 HOH HOH . I 5 HOH A 17 517 18 HOH HOH . I 5 HOH A 18 518 7 HOH HOH . I 5 HOH A 19 519 11 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 . . . B 2 2.566 -35.788 -9.852 1 57.37 ? C1 RET 401 A 1 HETATM 2 C C2 RET . . . B 2 3.57 -36.727 -9.205 1 53.91 ? C2 RET 401 A 1 HETATM 3 C C3 RET . . . B 2 3.621 -37.993 -10.035 1 53.25 ? C3 RET 401 A 1 HETATM 4 C C4 RET . . . B 2 2.297 -38.715 -9.853 1 51.52 ? C4 RET 401 A 1 HETATM 5 C C5 RET . . . B 2 1.095 -37.797 -9.975 1 53.52 ? C5 RET 401 A 1 HETATM 6 C C6 RET . . . B 2 1.208 -36.441 -9.943 1 53.9 ? C6 RET 401 A 1 HETATM 7 C C7 RET . . . B 2 0.1 -35.453 -10.072 1 50.84 ? C7 RET 401 A 1 HETATM 8 C C8 RET . . . B 2 -1.014 -35.617 -10.784 1 57.5 ? C8 RET 401 A 1 HETATM 9 C C9 RET . . . B 2 -2.071 -34.595 -10.849 1 55.91 ? C9 RET 401 A 1 HETATM 10 C C10 RET . . . B 2 -3.176 -34.88 -11.546 1 52.68 ? C10 RET 401 A 1 HETATM 11 C C11 RET . . . B 2 -4.277 -33.931 -11.655 1 55.96 ? C11 RET 401 A 1 HETATM 12 C C12 RET . . . B 2 -5.386 -34.343 -12.261 1 53.99 ? C12 RET 401 A 1 HETATM 13 C C13 RET . . . B 2 -6.55 -33.455 -12.412 1 59.72 ? C13 RET 401 A 1 HETATM 14 C C14 RET . . . B 2 -7.637 -33.9 -13.055 1 57.24 ? C14 RET 401 A 1 HETATM 15 C C15 RET . . . B 2 -8.793 -33.024 -13.21 1 65.78 ? C15 RET 401 A 1 HETATM 16 C C16 RET . . . B 2 2.467 -34.504 -9.035 1 51.62 ? C16 RET 401 A 1 HETATM 17 C C17 RET . . . B 2 3 -35.445 -11.273 1 55.04 ? C17 RET 401 A 1 HETATM 18 C C18 RET . . . B 2 -0.211 -38.541 -10.064 1 49.95 ? C18 RET 401 A 1 HETATM 19 C C19 RET . . . B 2 -1.92 -33.279 -10.144 1 50.85 ? C19 RET 401 A 1 HETATM 20 C C20 RET . . . B 2 -6.517 -32.065 -11.849 1 54.81 ? C20 RET 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #