data_3X3B # _model_server_result.job_id qArhoaHvNvl_mZXjCC5mIw _model_server_result.datetime_utc '2024-11-23 05:06:26' _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 3x3b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3X3B # _exptl.entry_id 3X3B _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 3X3B _cell.length_a 40.582 _cell.length_b 81.544 _cell.length_c 233.775 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X3B _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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_885 -x+3,-y+3,z -1 0 0 0 -1 0 0 0 1 121.746 244.632 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 255 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 255 _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 501 _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 1.447 _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 333 n n C1 C6 RET sing 334 n n C1 C16 RET sing 335 n n C1 C17 RET sing 336 n n C2 C3 RET sing 337 n n C2 H21 RET sing 338 n n C2 H22 RET sing 339 n n C3 C4 RET sing 340 n n C3 H31 RET sing 341 n n C3 H32 RET sing 342 n n C4 C5 RET sing 343 n n C4 H41 RET sing 344 n n C4 H42 RET sing 345 n n C5 C6 RET doub 346 n n C5 C18 RET sing 347 n n C6 C7 RET sing 348 n n C7 C8 RET doub 349 e n C7 H7 RET sing 350 n n C8 C9 RET sing 351 n n C8 H8 RET sing 352 n n C9 C10 RET doub 353 e n C9 C19 RET sing 354 n n C10 C11 RET sing 355 n n C10 H10 RET sing 356 n n C11 C12 RET doub 357 e n C11 H11 RET sing 358 n n C12 C13 RET sing 359 n n C12 H12 RET sing 360 n n C13 C14 RET doub 361 e n C13 C20 RET sing 362 n n C14 C15 RET sing 363 n n C14 H14 RET sing 364 n n C15 O1 RET doub 365 n n C15 H15 RET sing 366 n n C16 H161 RET sing 367 n n C16 H162 RET sing 368 n n C16 H163 RET sing 369 n n C17 H171 RET sing 370 n n C17 H172 RET sing 371 n n C17 H173 RET sing 372 n n C18 H181 RET sing 373 n n C18 H182 RET sing 374 n n C18 H183 RET sing 375 n n C19 H191 RET sing 376 n n C19 H192 RET sing 377 n n C19 H193 RET sing 378 n n C20 H201 RET sing 379 n n C20 H202 RET sing 380 n n C20 H203 RET sing 381 n n # _atom_sites.entry_id 3X3B _atom_sites.fract_transf_matrix[1][1] 0.024641 _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] 0.012263 _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] 0.004278 _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 1 501 501 RET RET . C 3 OLA A 1 502 601 OLA OLA . D 3 OLA A 1 503 602 OLA OLA . E 3 OLA A 1 504 603 OLA OLA . F 4 PEG A 1 505 701 PEG PEG . G 5 HOH A 1 901 901 HOH HOH . G 5 HOH A 2 902 902 HOH HOH . G 5 HOH A 3 903 903 HOH HOH . G 5 HOH A 4 904 904 HOH HOH . G 5 HOH A 5 905 905 HOH HOH . G 5 HOH A 6 906 906 HOH HOH . G 5 HOH A 7 907 907 HOH HOH . G 5 HOH A 8 908 908 HOH HOH . G 5 HOH A 9 909 909 HOH HOH . G 5 HOH A 10 910 910 HOH HOH . G 5 HOH A 11 911 911 HOH HOH . G 5 HOH A 12 912 912 HOH HOH . G 5 HOH A 13 913 913 HOH HOH . G 5 HOH A 14 914 914 HOH HOH . G 5 HOH A 15 915 915 HOH HOH . G 5 HOH A 16 916 916 HOH HOH . G 5 HOH A 17 917 917 HOH HOH . G 5 HOH A 18 918 918 HOH HOH . G 5 HOH A 19 919 919 HOH HOH . G 5 HOH A 20 920 920 HOH HOH . G 5 HOH A 21 921 921 HOH HOH . G 5 HOH A 22 922 922 HOH HOH . G 5 HOH A 23 923 923 HOH HOH . G 5 HOH A 24 924 924 HOH HOH . G 5 HOH A 25 925 925 HOH HOH . G 5 HOH A 26 926 926 HOH HOH . G 5 HOH A 27 927 927 HOH HOH . G 5 HOH A 28 928 928 HOH HOH . G 5 HOH A 29 929 929 HOH HOH . G 5 HOH A 30 930 930 HOH HOH . G 5 HOH A 31 931 931 HOH HOH . G 5 HOH A 32 932 932 HOH HOH . G 5 HOH A 33 933 933 HOH HOH . G 5 HOH A 34 934 934 HOH HOH . G 5 HOH A 35 935 935 HOH HOH . G 5 HOH A 36 936 936 HOH HOH . G 5 HOH A 37 937 937 HOH HOH . G 5 HOH A 38 938 938 HOH HOH . G 5 HOH A 39 939 939 HOH HOH . G 5 HOH A 40 940 940 HOH HOH . G 5 HOH A 41 941 941 HOH HOH . G 5 HOH A 42 942 942 HOH HOH . G 5 HOH A 43 943 943 HOH HOH . G 5 HOH A 44 944 944 HOH HOH . G 5 HOH A 45 945 945 HOH HOH . G 5 HOH A 46 946 946 HOH HOH . G 5 HOH A 47 947 947 HOH HOH . G 5 HOH A 48 948 948 HOH HOH . G 5 HOH A 49 949 949 HOH HOH . G 5 HOH A 50 950 950 HOH HOH . G 5 HOH A 51 951 951 HOH HOH . G 5 HOH A 52 952 952 HOH HOH . G 5 HOH A 53 953 953 HOH HOH . G 5 HOH A 54 954 954 HOH HOH . G 5 HOH A 55 955 955 HOH HOH . G 5 HOH A 56 956 956 HOH HOH . G 5 HOH A 57 957 957 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 62.946 96.483 260.846 1 35.11 ? C1 RET 501 A 1 HETATM 2 C C2 RET . . . B 2 63.467 95.363 259.934 1 33.71 ? C2 RET 501 A 1 HETATM 3 C C3 RET . . . B 2 62.73 94.042 260.078 1 37.99 ? C3 RET 501 A 1 HETATM 4 C C4 RET . . . B 2 62.816 93.543 261.506 1 33.34 ? C4 RET 501 A 1 HETATM 5 C C5 RET . . . B 2 62.561 94.614 262.532 1 37.41 ? C5 RET 501 A 1 HETATM 6 C C6 RET . . . B 2 62.571 95.924 262.232 1 31.57 ? C6 RET 501 A 1 HETATM 7 C C7 RET . . . B 2 62.136 96.883 263.313 1 27.13 ? C7 RET 501 A 1 HETATM 8 C C8 RET . . . B 2 62.043 98.211 263.319 1 26.99 ? C8 RET 501 A 1 HETATM 9 C C9 RET . . . B 2 61.587 99.071 264.39 1 35.24 ? C9 RET 501 A 1 HETATM 10 C C10 RET . . . B 2 61.543 100.408 264.181 1 34.47 ? C10 RET 501 A 1 HETATM 11 C C11 RET . . . B 2 61.1 101.419 265.104 1 32.81 ? C11 RET 501 A 1 HETATM 12 C C12 RET . . . B 2 61.078 102.711 264.796 1 34.24 ? C12 RET 501 A 1 HETATM 13 C C13 RET . . . B 2 60.546 103.792 265.596 1 34.97 ? C13 RET 501 A 1 HETATM 14 C C14 RET . . . B 2 60.461 105.028 265.051 1 35.34 ? C14 RET 501 A 1 HETATM 15 C C15 RET . . . B 2 59.933 106.128 265.811 1 34.45 ? C15 RET 501 A 1 HETATM 16 C C16 RET . . . B 2 61.735 97.125 260.161 1 30.37 ? C16 RET 501 A 1 HETATM 17 C C17 RET . . . B 2 64.066 97.529 260.969 1 34.84 ? C17 RET 501 A 1 HETATM 18 C C18 RET . . . B 2 62.343 94.062 263.918 1 35.59 ? C18 RET 501 A 1 HETATM 19 C C19 RET . . . B 2 61.145 98.432 265.681 1 30.36 ? C19 RET 501 A 1 HETATM 20 C C20 RET . . . B 2 60.103 103.486 267 1 28.55 ? C20 RET 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #