data_6RNJ # _model_server_result.job_id v5w5e5if4TjDRcdUDbTCUQ _model_server_result.datetime_utc '2024-11-13 08:41:17' _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 6rnj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6RNJ # _exptl.entry_id 6RNJ _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 6RNJ _cell.length_a 62 _cell.length_b 62 _cell.length_c 110.3 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _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 _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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 31 53.693575 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -31 53.693575 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 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 1.408 _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 243 n n C1 C6 RET sing 244 n n C1 C16 RET sing 245 n n C1 C17 RET sing 246 n n C2 C3 RET sing 247 n n C2 H21 RET sing 248 n n C2 H22 RET sing 249 n n C3 C4 RET sing 250 n n C3 H31 RET sing 251 n n C3 H32 RET sing 252 n n C4 C5 RET sing 253 n n C4 H41 RET sing 254 n n C4 H42 RET sing 255 n n C5 C6 RET doub 256 n n C5 C18 RET sing 257 n n C6 C7 RET sing 258 n n C7 C8 RET doub 259 e n C7 H7 RET sing 260 n n C8 C9 RET sing 261 n n C8 H8 RET sing 262 n n C9 C10 RET doub 263 e n C9 C19 RET sing 264 n n C10 C11 RET sing 265 n n C10 H10 RET sing 266 n n C11 C12 RET doub 267 e n C11 H11 RET sing 268 n n C12 C13 RET sing 269 n n C12 H12 RET sing 270 n n C13 C14 RET doub 271 e n C13 C20 RET sing 272 n n C14 C15 RET sing 273 n n C14 H14 RET sing 274 n n C15 O1 RET doub 275 n n C15 H15 RET sing 276 n n C16 H161 RET sing 277 n n C16 H162 RET sing 278 n n C16 H163 RET sing 279 n n C17 H171 RET sing 280 n n C17 H172 RET sing 281 n n C17 H173 RET sing 282 n n C18 H181 RET sing 283 n n C18 H182 RET sing 284 n n C18 H183 RET sing 285 n n C19 H191 RET sing 286 n n C19 H192 RET sing 287 n n C19 H193 RET sing 288 n n C20 H201 RET sing 289 n n C20 H202 RET sing 290 n n C20 H203 RET sing 291 n n # _atom_sites.entry_id 6RNJ _atom_sites.fract_transf_matrix[1][1] 0.016129 _atom_sites.fract_transf_matrix[1][2] 0.009312 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018624 _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] 0.009066 _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 HOH A 1 453 453 HOH HOH . C 3 HOH A 2 458 6 HOH HOH . C 3 HOH A 3 406 406 HOH HOH . C 3 HOH A 4 451 451 HOH HOH . C 3 HOH A 5 403 403 HOH HOH . C 3 HOH A 6 456 456 HOH HOH . C 3 HOH A 7 457 457 HOH HOH . C 3 HOH A 8 404 404 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 14.957 45.844 29.803 1 71.14 ? C1 RET 501 A 1 HETATM 2 C C2 RET . . . B 2 14.39 46.666 28.636 1 69.18 ? C2 RET 501 A 1 HETATM 3 C C3 RET . . . B 2 15.141 47.967 28.428 1 77.74 ? C3 RET 501 A 1 HETATM 4 C C4 RET . . . B 2 15.046 48.833 29.662 1 71.3 ? C4 RET 501 A 1 HETATM 5 C C5 RET . . . B 2 15.199 48.077 30.956 1 65.71 ? C5 RET 501 A 1 HETATM 6 C C6 RET . . . B 2 15.187 46.736 31.024 1 69.71 ? C6 RET 501 A 1 HETATM 7 C C7 RET . . . B 2 15.476 46.063 32.321 1 66.9 ? C7 RET 501 A 1 HETATM 8 C C8 RET . . . B 2 15.973 44.849 32.561 1 64.1 ? C8 RET 501 A 1 HETATM 9 C C9 RET . . . B 2 16.268 44.283 33.874 1 61.38 ? C9 RET 501 A 1 HETATM 10 C C10 RET . . . B 2 16.572 42.965 33.97 1 57.73 ? C10 RET 501 A 1 HETATM 11 C C11 RET . . . B 2 16.97 42.246 35.141 1 70.07 ? C11 RET 501 A 1 HETATM 12 C C12 RET . . . B 2 17.291 40.944 35.157 1 63.99 ? C12 RET 501 A 1 HETATM 13 C C13 RET . . . B 2 17.706 40.175 36.311 1 76.64 ? C13 RET 501 A 1 HETATM 14 C C14 RET . . . B 2 17.981 38.855 36.179 1 73.78 ? C14 RET 501 A 1 HETATM 15 C C15 RET . . . B 2 17.896 38.113 34.946 1 81.2 ? C15 RET 501 A 1 HETATM 16 C C16 RET . . . B 2 16.276 45.218 29.335 1 59.56 ? C16 RET 501 A 1 HETATM 17 C C17 RET . . . B 2 13.961 44.731 30.12 1 51.09 ? C17 RET 501 A 1 HETATM 18 C C18 RET . . . B 2 15.318 48.98 32.141 1 73.75 ? C18 RET 501 A 1 HETATM 19 C C19 RET . . . B 2 16.266 45.213 35.066 1 55.66 ? C19 RET 501 A 1 HETATM 20 C C20 RET . . . B 2 17.812 40.888 37.619 1 79.71 ? C20 RET 501 A 1 HETATM 21 H H21 RET . . . B 2 13.334 46.877 28.801 1 83.12 ? H21 RET 501 A 1 HETATM 22 H H22 RET . . . B 2 14.412 46.082 27.717 1 83.12 ? H22 RET 501 A 1 HETATM 23 H H31 RET . . . B 2 14.75 48.498 27.561 1 93.39 ? H31 RET 501 A 1 HETATM 24 H H32 RET . . . B 2 16.183 47.77 28.183 1 93.39 ? H32 RET 501 A 1 HETATM 25 H H41 RET . . . B 2 14.092 49.359 29.674 1 85.67 ? H41 RET 501 A 1 HETATM 26 H H42 RET . . . B 2 15.801 49.617 29.624 1 85.67 ? H42 RET 501 A 1 HETATM 27 H H7 RET . . . B 2 15.228 46.695 33.172 1 80.39 ? H7 RET 501 A 1 HETATM 28 H H8 RET . . . B 2 16.187 44.202 31.712 1 77.03 ? H8 RET 501 A 1 HETATM 29 H H10 RET . . . B 2 16.515 42.362 33.065 1 69.38 ? H10 RET 501 A 1 HETATM 30 H H11 RET . . . B 2 16.998 42.838 36.054 1 84.19 ? H11 RET 501 A 1 HETATM 31 H H12 RET . . . B 2 17.243 40.382 34.225 1 76.89 ? H12 RET 501 A 1 HETATM 32 H H14 RET . . . B 2 18.293 38.272 37.044 1 88.65 ? H14 RET 501 A 1 HETATM 33 H H161 RET . . . B 2 17.12 45.896 29.458 1 71.58 ? H161 RET 501 A 1 HETATM 34 H H162 RET . . . B 2 16.25 44.942 28.282 1 71.58 ? H162 RET 501 A 1 HETATM 35 H H163 RET . . . B 2 16.521 44.313 29.889 1 71.58 ? H163 RET 501 A 1 HETATM 36 H H171 RET . . . B 2 14.4 43.972 30.766 1 61.42 ? H171 RET 501 A 1 HETATM 37 H H172 RET . . . B 2 13.62 44.229 29.216 1 61.42 ? H172 RET 501 A 1 HETATM 38 H H173 RET . . . B 2 13.078 45.117 30.629 1 61.42 ? H173 RET 501 A 1 HETATM 39 H H181 RET . . . B 2 15.384 50.021 31.826 1 88.6 ? H181 RET 501 A 1 HETATM 40 H H182 RET . . . B 2 14.453 48.875 32.793 1 88.6 ? H182 RET 501 A 1 HETATM 41 H H183 RET . . . B 2 16.211 48.742 32.717 1 88.6 ? H183 RET 501 A 1 HETATM 42 H H191 RET . . . B 2 15.35 45.142 35.651 1 66.9 ? H191 RET 501 A 1 HETATM 43 H H192 RET . . . B 2 17.083 45.01 35.757 1 66.9 ? H192 RET 501 A 1 HETATM 44 H H193 RET . . . B 2 16.363 46.259 34.781 1 66.9 ? H193 RET 501 A 1 HETATM 45 H H201 RET . . . B 2 18.697 41.522 37.645 1 95.76 ? H201 RET 501 A 1 HETATM 46 H H202 RET . . . B 2 16.941 41.519 37.789 1 95.76 ? H202 RET 501 A 1 HETATM 47 H H203 RET . . . B 2 17.882 40.18 38.443 1 95.76 ? H203 RET 501 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 47 #