data_1VGO # _model_server_result.job_id 54rcuAMzIkjVAjdrw7BHDA _model_server_result.datetime_utc '2024-11-02 05:29:18' _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 1vgo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":261}' # _entry.id 1VGO # _exptl.entry_id 1VGO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 2 _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 1VGO _cell.length_a 122.88 _cell.length_b 139.48 _cell.length_c 108.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VGO _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _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,I,J,K,L,M,N,O,P,Q,R,S,T,U _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 M N N ? 4 S N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 221 A LYS 221 1_555 M C15 RET . A RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale2 B NZ LYS 221 B LYS 221 1_555 S C15 RET . B RET 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? # _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 294 n n C1 C6 RET sing 295 n n C1 C16 RET sing 296 n n C1 C17 RET sing 297 n n C2 C3 RET sing 298 n n C2 H21 RET sing 299 n n C2 H22 RET sing 300 n n C3 C4 RET sing 301 n n C3 H31 RET sing 302 n n C3 H32 RET sing 303 n n C4 C5 RET sing 304 n n C4 H41 RET sing 305 n n C4 H42 RET sing 306 n n C5 C6 RET doub 307 n n C5 C18 RET sing 308 n n C6 C7 RET sing 309 n n C7 C8 RET doub 310 e n C7 H7 RET sing 311 n n C8 C9 RET sing 312 n n C8 H8 RET sing 313 n n C9 C10 RET doub 314 e n C9 C19 RET sing 315 n n C10 C11 RET sing 316 n n C10 H10 RET sing 317 n n C11 C12 RET doub 318 e n C11 H11 RET sing 319 n n C12 C13 RET sing 320 n n C12 H12 RET sing 321 n n C13 C14 RET doub 322 e n C13 C20 RET sing 323 n n C14 C15 RET sing 324 n n C14 H14 RET sing 325 n n C15 O1 RET doub 326 n n C15 H15 RET sing 327 n n C16 H161 RET sing 328 n n C16 H162 RET sing 329 n n C16 H163 RET sing 330 n n C17 H171 RET sing 331 n n C17 H172 RET sing 332 n n C17 H173 RET sing 333 n n C18 H181 RET sing 334 n n C18 H182 RET sing 335 n n C18 H183 RET sing 336 n n C19 H191 RET sing 337 n n C19 H192 RET sing 338 n n C19 H193 RET sing 339 n n C20 H201 RET sing 340 n n C20 H202 RET sing 341 n n C20 H203 RET sing 342 n n # _atom_sites.entry_id 1VGO _atom_sites.fract_transf_matrix[1][1] 0.008138 _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] 0.007169 _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] 0.009251 _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 C 2 BNG A 1 301 301 BNG BNG . D 2 BNG A 1 302 302 BNG BNG . E 2 BNG A 1 303 303 BNG BNG . F 2 BNG A 1 304 304 BNG BNG . G 2 BNG A 1 305 305 BNG BNG . H 2 BNG A 1 306 306 BNG BNG . I 2 BNG A 1 307 307 BNG BNG . J 2 BNG A 1 308 308 BNG BNG . K 2 BNG A 1 309 309 BNG BNG . L 3 SO4 A 1 400 400 SO4 SO4 . M 4 RET A 1 260 260 RET RET . N 2 BNG B 1 310 310 BNG BNG . O 2 BNG B 1 311 311 BNG BNG . P 2 BNG B 1 312 312 BNG BNG . Q 3 SO4 B 1 401 401 SO4 SO4 . R 3 SO4 B 1 402 402 SO4 SO4 . S 4 RET B 1 261 261 RET RET . T 5 HOH A 1 501 501 HOH HOH . T 5 HOH A 2 502 502 HOH HOH . T 5 HOH A 3 503 503 HOH HOH . T 5 HOH A 4 504 504 HOH HOH . T 5 HOH A 5 505 505 HOH HOH . T 5 HOH A 6 506 506 HOH HOH . T 5 HOH A 7 507 507 HOH HOH . T 5 HOH A 8 508 508 HOH HOH . T 5 HOH A 9 509 509 HOH HOH . T 5 HOH A 10 510 510 HOH HOH . T 5 HOH A 11 511 511 HOH HOH . T 5 HOH A 12 512 512 HOH HOH . T 5 HOH A 13 513 513 HOH HOH . T 5 HOH A 14 701 701 HOH HOH . T 5 HOH A 15 702 702 HOH HOH . T 5 HOH A 16 705 705 HOH HOH . U 5 HOH B 1 601 601 HOH HOH . U 5 HOH B 2 602 602 HOH HOH . U 5 HOH B 3 603 603 HOH HOH . U 5 HOH B 4 605 605 HOH HOH . U 5 HOH B 5 606 606 HOH HOH . U 5 HOH B 6 607 607 HOH HOH . U 5 HOH B 7 608 608 HOH HOH . U 5 HOH B 8 700 700 HOH HOH . U 5 HOH B 9 703 703 HOH HOH . U 5 HOH B 10 704 704 HOH HOH . U 5 HOH B 11 706 706 HOH HOH . U 5 HOH B 12 707 707 HOH HOH . U 5 HOH B 13 708 708 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 . . . S 4 23.52 48.264 -0.608 1 52.72 ? C1 RET 261 B 1 HETATM 2 C C2 RET . . . S 4 24.146 49.327 -1.622 1 52.52 ? C2 RET 261 B 1 HETATM 3 C C3 RET . . . S 4 25.595 49.559 -1.491 1 54.89 ? C3 RET 261 B 1 HETATM 4 C C4 RET . . . S 4 25.958 50.042 -0.079 1 51.07 ? C4 RET 261 B 1 HETATM 5 C C5 RET . . . S 4 25.501 49.095 1.015 1 50.34 ? C5 RET 261 B 1 HETATM 6 C C6 RET . . . S 4 24.359 48.216 0.85 1 52.32 ? C6 RET 261 B 1 HETATM 7 C C7 RET . . . S 4 23.956 47.254 2.017 1 52.01 ? C7 RET 261 B 1 HETATM 8 C C8 RET . . . S 4 22.913 46.411 1.936 1 50.08 ? C8 RET 261 B 1 HETATM 9 C C9 RET . . . S 4 22.669 45.381 2.932 1 49.36 ? C9 RET 261 B 1 HETATM 10 C C10 RET . . . S 4 21.581 44.6 2.697 1 48.94 ? C10 RET 261 B 1 HETATM 11 C C11 RET . . . S 4 21.162 43.502 3.51 1 49.26 ? C11 RET 261 B 1 HETATM 12 C C12 RET . . . S 4 20.081 42.874 3.11 1 49.2 ? C12 RET 261 B 1 HETATM 13 C C13 RET . . . S 4 19.465 41.753 3.822 1 51.28 ? C13 RET 261 B 1 HETATM 14 C C14 RET . . . S 4 18.338 41.242 3.225 1 50.87 ? C14 RET 261 B 1 HETATM 15 C C15 RET . . . S 4 17.42 40.276 3.784 1 49.77 ? C15 RET 261 B 1 HETATM 16 C C16 RET . . . S 4 22.046 48.677 -0.427 1 52.79 ? C16 RET 261 B 1 HETATM 17 C C17 RET . . . S 4 23.61 46.934 -1.374 1 51.14 ? C17 RET 261 B 1 HETATM 18 C C18 RET . . . S 4 26.311 49.116 2.299 1 50.44 ? C18 RET 261 B 1 HETATM 19 C C19 RET . . . S 4 23.582 45.158 4.149 1 47.87 ? C19 RET 261 B 1 HETATM 20 C C20 RET . . . S 4 19.981 41.286 5.194 1 50.39 ? C20 RET 261 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #