data_1VJM # _model_server_result.job_id 0-HEP_egnajeywfg-2gXqQ _model_server_result.datetime_utc '2024-10-18 18:20:19' _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 1vjm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1VJM # _exptl.entry_id 1VJM _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 1VJM _cell.length_a 60.87 _cell.length_b 60.87 _cell.length_c 109.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VJM _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PQS monomeric 1 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 1 1,2,3 A,B,C 2 1 # 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 30.435 52.714966 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 -30.435 52.714966 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 216 _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 300 _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 1.308 _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 1VJM _atom_sites.fract_transf_matrix[1][1] 0.016428 _atom_sites.fract_transf_matrix[1][2] 0.009485 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01897 _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] 0.009132 _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 1 300 300 RET RET . C 3 HOH A 1 400 400 HOH WAT . C 3 HOH A 2 401 401 HOH WAT . C 3 HOH A 3 402 402 HOH WAT . C 3 HOH A 4 403 403 HOH WAT . C 3 HOH A 5 404 404 HOH WAT . C 3 HOH A 6 405 405 HOH WAT . C 3 HOH A 7 406 406 HOH WAT . C 3 HOH A 8 407 407 HOH WAT . C 3 HOH A 9 408 408 HOH WAT . C 3 HOH A 10 409 409 HOH WAT . C 3 HOH A 11 410 410 HOH WAT . C 3 HOH A 12 412 412 HOH WAT . C 3 HOH A 13 414 414 HOH WAT . C 3 HOH A 14 424 424 HOH WAT . C 3 HOH A 15 425 425 HOH WAT . C 3 HOH A 16 427 427 HOH WAT . C 3 HOH A 17 431 431 HOH WAT . C 3 HOH A 18 432 432 HOH WAT . C 3 HOH A 19 433 433 HOH WAT . C 3 HOH A 20 437 437 HOH WAT . C 3 HOH A 21 438 438 HOH WAT . C 3 HOH A 22 439 439 HOH WAT . C 3 HOH A 23 441 441 HOH WAT . C 3 HOH A 24 442 442 HOH WAT . C 3 HOH A 25 443 443 HOH WAT . C 3 HOH A 26 444 444 HOH WAT . # 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 14.76 45.136 -0.277 0.5 36.36 ? C1 RET 300 A 1 HETATM 2 C C2 RET . . . B 2 14.059 46.1 -1.285 0.5 35.45 ? C2 RET 300 A 1 HETATM 3 C C3 RET . . . B 2 14.726 47.457 -1.383 0.5 36.83 ? C3 RET 300 A 1 HETATM 4 C C4 RET . . . B 2 14.783 48.171 -0.038 0.5 38.14 ? C4 RET 300 A 1 HETATM 5 C C5 RET . . . B 2 15.132 47.25 1.151 0.5 36.88 ? C5 RET 300 A 1 HETATM 6 C C6 RET . . . B 2 15.136 45.858 1.075 0.5 36.7 ? C6 RET 300 A 1 HETATM 7 C C7 RET . . . B 2 15.547 45.101 2.274 0.5 34.9 ? C7 RET 300 A 1 HETATM 8 C C8 RET . . . B 2 15.777 43.836 2.703 0.5 35.04 ? C8 RET 300 A 1 HETATM 9 C C9 RET . . . B 2 16.298 43.285 3.911 0.5 36.18 ? C9 RET 300 A 1 HETATM 10 C C10 RET . . . B 2 16.405 41.94 3.783 0.5 37.43 ? C10 RET 300 A 1 HETATM 11 C C11 RET . . . B 2 16.947 41.034 4.727 0.5 39.16 ? C11 RET 300 A 1 HETATM 12 C C12 RET . . . B 2 17.035 39.716 4.562 0.5 36.99 ? C12 RET 300 A 1 HETATM 13 C C13 RET . . . B 2 17.499 38.72 5.48 0.5 39.84 ? C13 RET 300 A 1 HETATM 14 C C14 RET . . . B 2 17.365 37.496 4.917 0.5 39.58 ? C14 RET 300 A 1 HETATM 15 C C15 RET . . . B 2 17.609 36.216 5.337 0.5 41.6 ? C15 RET 300 A 1 HETATM 16 C C16 RET . . . B 2 13.735 44.014 -0.228 0.5 35.38 ? C16 RET 300 A 1 HETATM 17 C C17 RET . . . B 2 16.059 44.583 -0.949 0.5 35.84 ? C17 RET 300 A 1 HETATM 18 C C18 RET . . . B 2 15.414 48.179 2.314 0.5 39.41 ? C18 RET 300 A 1 HETATM 19 C C19 RET . . . B 2 16.734 44.181 5.046 0.5 34.18 ? C19 RET 300 A 1 HETATM 20 C C20 RET . . . B 2 17.988 39.039 6.874 0.5 38.46 ? C20 RET 300 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 80 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 690 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #