data_5ZIL # _model_server_result.job_id xaNcKcTdldc0nFKt-o25yw _model_server_result.datetime_utc '2024-11-08 13:46:18' _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 5zil # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":250}' # _entry.id 5ZIL # _exptl.entry_id 5ZIL _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 120 _cell.entry_id 5ZIL _cell.length_a 60.59 _cell.length_b 60.59 _cell.length_c 110.74 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZIL _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_635 -y+1,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.18 -104.944958 0 3 'crystal symmetry operation' 3_865 -x+y+3,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 151.475 52.472479 0 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 212 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 250 _struct_conn.ptnr2_symmetry 1_555 _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 1.338 _struct_conn.pdbx_value_order ? # _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 376 n n C1 C6 RET sing 377 n n C1 C16 RET sing 378 n n C1 C17 RET sing 379 n n C2 C3 RET sing 380 n n C2 H21 RET sing 381 n n C2 H22 RET sing 382 n n C3 C4 RET sing 383 n n C3 H31 RET sing 384 n n C3 H32 RET sing 385 n n C4 C5 RET sing 386 n n C4 H41 RET sing 387 n n C4 H42 RET sing 388 n n C5 C6 RET doub 389 n n C5 C18 RET sing 390 n n C6 C7 RET sing 391 n n C7 C8 RET doub 392 e n C7 H7 RET sing 393 n n C8 C9 RET sing 394 n n C8 H8 RET sing 395 n n C9 C10 RET doub 396 e n C9 C19 RET sing 397 n n C10 C11 RET sing 398 n n C10 H10 RET sing 399 n n C11 C12 RET doub 400 e n C11 H11 RET sing 401 n n C12 C13 RET sing 402 n n C12 H12 RET sing 403 n n C13 C14 RET doub 404 e n C13 C20 RET sing 405 n n C14 C15 RET sing 406 n n C14 H14 RET sing 407 n n C15 O1 RET doub 408 n n C15 H15 RET sing 409 n n C16 H161 RET sing 410 n n C16 H162 RET sing 411 n n C16 H163 RET sing 412 n n C17 H171 RET sing 413 n n C17 H172 RET sing 414 n n C17 H173 RET sing 415 n n C18 H181 RET sing 416 n n C18 H182 RET sing 417 n n C18 H183 RET sing 418 n n C19 H191 RET sing 419 n n C19 H192 RET sing 420 n n C19 H193 RET sing 421 n n C20 H201 RET sing 422 n n C20 H202 RET sing 423 n n C20 H203 RET sing 424 n n # _atom_sites.entry_id 5ZIL _atom_sites.fract_transf_matrix[1][1] 0.016504 _atom_sites.fract_transf_matrix[1][2] 0.009529 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019058 _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] 0.00903 _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 1 250 250 RET RET . C 3 L2P A 1 270 270 L2P L2P . D 3 L2P A 1 290 290 L2P L2P . E 3 L2P A 1 300 300 L2P L2P . F 3 L2P A 1 310 310 L2P L2P . G 4 HOH A 1 402 402 HOH HOH . G 4 HOH A 2 401 401 HOH HOH . G 4 HOH A 3 406 406 HOH HOH . G 4 HOH A 4 513 513 HOH HOH . G 4 HOH A 5 512 512 HOH HOH . G 4 HOH A 6 502 502 HOH HOH . G 4 HOH A 7 514 514 HOH HOH . G 4 HOH A 8 403 403 HOH HOH . G 4 HOH A 9 404 404 HOH HOH . G 4 HOH A 10 415 415 HOH HOH . G 4 HOH A 11 420 420 HOH HOH . G 4 HOH A 12 411 411 HOH HOH . G 4 HOH A 13 412 412 HOH HOH . G 4 HOH A 14 501 501 HOH HOH . G 4 HOH A 15 407 407 HOH HOH . G 4 HOH A 16 511 511 HOH HOH . G 4 HOH A 17 405 405 HOH HOH . G 4 HOH A 18 419 419 HOH HOH . G 4 HOH A 19 416 416 HOH HOH . G 4 HOH A 20 450 450 HOH HOH . G 4 HOH A 21 451 451 HOH HOH . G 4 HOH A 22 452 452 HOH HOH . G 4 HOH A 23 453 453 HOH HOH . G 4 HOH A 24 454 454 HOH HOH . G 4 HOH A 25 455 455 HOH HOH . G 4 HOH A 26 456 456 HOH HOH . G 4 HOH A 27 457 457 HOH HOH . G 4 HOH A 28 458 458 HOH HOH . G 4 HOH A 29 459 459 HOH HOH . G 4 HOH A 30 460 460 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 75.944 -7.325 -21.001 1 14.06 ? C1 RET 250 A 1 HETATM 2 C C2 RET . . . B 2 76.012 -6.339 -19.811 1 14.52 ? C2 RET 250 A 1 HETATM 3 C C3 RET . . . B 2 76.86 -5.126 -20.062 1 13.99 ? C3 RET 250 A 1 HETATM 4 C C4 RET . . . B 2 76.236 -4.365 -21.187 1 13.62 ? C4 RET 250 A 1 HETATM 5 C C5 RET . . . B 2 75.816 -5.232 -22.333 1 13.24 ? C5 RET 250 A 1 HETATM 6 C C6 RET . . . B 2 75.766 -6.602 -22.329 1 13.57 ? C6 RET 250 A 1 HETATM 7 C C7 RET . . . B 2 75.355 -7.304 -23.544 1 13.56 ? C7 RET 250 A 1 HETATM 8 C C8 RET . . . B 2 75.282 -8.67 -23.786 1 13.38 ? C8 RET 250 A 1 HETATM 9 C C9 RET . . . B 2 74.697 -9.238 -24.971 1 12.79 ? C9 RET 250 A 1 HETATM 10 C C10 RET . . . B 2 74.554 -10.605 -24.856 1 13.25 ? C10 RET 250 A 1 HETATM 11 C C11 RET . . . B 2 74.018 -11.463 -25.904 1 12.96 ? C11 RET 250 A 1 HETATM 12 C C12 RET . . . B 2 73.85 -12.801 -25.617 1 13.54 ? C12 RET 250 A 1 HETATM 13 C C13 RET . . . B 2 73.416 -13.82 -26.552 1 14.05 ? C13 RET 250 A 1 HETATM 14 C C14 RET . . . B 2 73.492 -15.096 -25.977 1 14.15 ? C14 RET 250 A 1 HETATM 15 C C15 RET . . . B 2 73.607 -16.212 -26.879 1 13.74 ? C15 RET 250 A 1 HETATM 16 C C16 RET . . . B 2 77.235 -8.14 -21.141 1 14.71 ? C16 RET 250 A 1 HETATM 17 C C17 RET . . . B 2 74.756 -8.22 -20.577 1 14.75 ? C17 RET 250 A 1 HETATM 18 C C18 RET . . . B 2 75.75 -4.4 -23.618 1 13.42 ? C18 RET 250 A 1 HETATM 19 C C19 RET . . . B 2 74.368 -8.484 -26.178 1 13.38 ? C19 RET 250 A 1 HETATM 20 C C20 RET . . . B 2 73.04 -13.385 -27.884 1 14.7 ? C20 RET 250 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #