data_6NWD # _model_server_result.job_id 5gVJ6zYs7qdjli2FNmsk1A _model_server_result.datetime_utc '2024-11-25 10:37:23' _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 6nwd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1301}' # _entry.id 6NWD # _exptl.entry_id 6NWD _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 6NWD _cell.length_a 54.25 _cell.length_b 129.25 _cell.length_c 82.65 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _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 _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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 41.325 # _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 257 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 257 _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 1301 _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 1.43 _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 450 n n C1 C6 RET sing 451 n n C1 C16 RET sing 452 n n C1 C17 RET sing 453 n n C2 C3 RET sing 454 n n C2 H21 RET sing 455 n n C2 H22 RET sing 456 n n C3 C4 RET sing 457 n n C3 H31 RET sing 458 n n C3 H32 RET sing 459 n n C4 C5 RET sing 460 n n C4 H41 RET sing 461 n n C4 H42 RET sing 462 n n C5 C6 RET doub 463 n n C5 C18 RET sing 464 n n C6 C7 RET sing 465 n n C7 C8 RET doub 466 e n C7 H7 RET sing 467 n n C8 C9 RET sing 468 n n C8 H8 RET sing 469 n n C9 C10 RET doub 470 e n C9 C19 RET sing 471 n n C10 C11 RET sing 472 n n C10 H10 RET sing 473 n n C11 C12 RET doub 474 e n C11 H11 RET sing 475 n n C12 C13 RET sing 476 n n C12 H12 RET sing 477 n n C13 C14 RET doub 478 e n C13 C20 RET sing 479 n n C14 C15 RET sing 480 n n C14 H14 RET sing 481 n n C15 O1 RET doub 482 n n C15 H15 RET sing 483 n n C16 H161 RET sing 484 n n C16 H162 RET sing 485 n n C16 H163 RET sing 486 n n C17 H171 RET sing 487 n n C17 H172 RET sing 488 n n C17 H173 RET sing 489 n n C18 H181 RET sing 490 n n C18 H182 RET sing 491 n n C18 H183 RET sing 492 n n C19 H191 RET sing 493 n n C19 H192 RET sing 494 n n C19 H193 RET sing 495 n n C20 H201 RET sing 496 n n C20 H202 RET sing 497 n n C20 H203 RET sing 498 n n # _atom_sites.entry_id 6NWD _atom_sites.fract_transf_matrix[1][1] 0.018433 _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] 0.007737 _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] 0.012099 _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 1301 1301 RET RET . C 3 PX4 A 1 1302 1401 PX4 PX4 . D 3 PX4 A 1 1303 1402 PX4 PX4 . E 3 PX4 A 1 1304 1403 PX4 PX4 . F 4 D10 A 1 1305 1404 D10 D10 . G 5 D12 A 1 1306 1405 D12 D12 . H 6 HOH A 1 1401 402 HOH HOH . H 6 HOH A 2 1402 411 HOH HOH . H 6 HOH A 3 1403 502 HOH HOH . H 6 HOH A 4 1404 501 HOH HOH . H 6 HOH A 5 1405 414 HOH HOH . H 6 HOH A 6 1406 420 HOH HOH . H 6 HOH A 7 1407 413 HOH HOH . H 6 HOH A 8 1408 412 HOH HOH . H 6 HOH A 9 1409 417 HOH HOH . H 6 HOH A 10 1410 418 HOH HOH . H 6 HOH A 11 1411 419 HOH HOH . H 6 HOH A 12 1412 410 HOH HOH . H 6 HOH A 13 1413 416 HOH HOH . H 6 HOH A 14 1414 415 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 14.261 28.301 40.535 1 24.93 ? C1 RET 1301 A 1 HETATM 2 C C2 RET . . . B 2 14.447 27.03 41.568 1 25.04 ? C2 RET 1301 A 1 HETATM 3 C C3 RET . . . B 2 14.318 27.258 42.913 1 24.69 ? C3 RET 1301 A 1 HETATM 4 C C4 RET . . . B 2 13.163 28.367 43.245 1 23.83 ? C4 RET 1301 A 1 HETATM 5 C C5 RET . . . B 2 13.532 29.584 42.63 1 24.48 ? C5 RET 1301 A 1 HETATM 6 C C6 RET . . . B 2 13.664 29.483 41.076 1 20.17 ? C6 RET 1301 A 1 HETATM 7 C C7 RET . . . B 2 12.915 30.475 40.197 1 23.1 ? C7 RET 1301 A 1 HETATM 8 C C8 RET . . . B 2 13.6 31.226 39.302 1 20.51 ? C8 RET 1301 A 1 HETATM 9 C C9 RET . . . B 2 12.965 32.237 38.37 1 17.98 ? C9 RET 1301 A 1 HETATM 10 C C10 RET . . . B 2 13.197 32.129 37.045 1 23.69 ? C10 RET 1301 A 1 HETATM 11 C C11 RET . . . B 2 12.626 33.104 36.037 1 23.67 ? C11 RET 1301 A 1 HETATM 12 C C12 RET . . . B 2 13.056 32.998 34.761 1 22.05 ? C12 RET 1301 A 1 HETATM 13 C C13 RET . . . B 2 12.582 33.922 33.66 1 22.73 ? C13 RET 1301 A 1 HETATM 14 C C14 RET . . . B 2 12.737 33.555 32.371 1 26.94 ? C14 RET 1301 A 1 HETATM 15 C C15 RET . . . B 2 12.284 34.474 31.262 1 24.65 ? C15 RET 1301 A 1 HETATM 16 C C16 RET . . . B 2 15.556 28.597 39.799 1 23.97 ? C16 RET 1301 A 1 HETATM 17 C C17 RET . . . B 2 13.406 27.799 39.39 1 25.42 ? C17 RET 1301 A 1 HETATM 18 C C18 RET . . . B 2 13.201 30.911 43.281 1 26.45 ? C18 RET 1301 A 1 HETATM 19 C C19 RET . . . B 2 12.106 33.352 38.925 1 21.89 ? C19 RET 1301 A 1 HETATM 20 C C20 RET . . . B 2 11.965 35.26 34 1 33.31 ? C20 RET 1301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #