data_2J4Y # _model_server_result.job_id uRZxO13Ywk-h7BfLV5aihw _model_server_result.datetime_utc '2024-11-16 12:25:49' _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 2j4y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1296}' # _entry.id 2J4Y # _exptl.entry_id 2J4Y _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 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 120 _cell.entry_id 2J4Y _cell.length_a 109.3 _cell.length_b 109.3 _cell.length_c 77.7 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J4Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 ? 2 C N N ? 2 E 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 disulf ? disulf1 A SG CYS 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 B SG CYS 3 B CYS 2 1_555 B SG CYS 283 B CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 111 B CYS 110 1_555 B SG CYS 188 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 D C1 NAG . A NAG 1327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale3 A NZ LYS 297 A LYS 296 1_555 C C15 RET . A RET 1296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? covale ? covale4 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 B ND2 ASN 16 B ASN 15 1_555 F C1 NAG . B NAG 1327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale6 B NZ LYS 297 B LYS 296 1_555 E C15 RET . B RET 1296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? # _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 311 n n C1 C6 RET sing 312 n n C1 C16 RET sing 313 n n C1 C17 RET sing 314 n n C2 C3 RET sing 315 n n C2 H21 RET sing 316 n n C2 H22 RET sing 317 n n C3 C4 RET sing 318 n n C3 H31 RET sing 319 n n C3 H32 RET sing 320 n n C4 C5 RET sing 321 n n C4 H41 RET sing 322 n n C4 H42 RET sing 323 n n C5 C6 RET doub 324 n n C5 C18 RET sing 325 n n C6 C7 RET sing 326 n n C7 C8 RET doub 327 e n C7 H7 RET sing 328 n n C8 C9 RET sing 329 n n C8 H8 RET sing 330 n n C9 C10 RET doub 331 e n C9 C19 RET sing 332 n n C10 C11 RET sing 333 n n C10 H10 RET sing 334 n n C11 C12 RET doub 335 e n C11 H11 RET sing 336 n n C12 C13 RET sing 337 n n C12 H12 RET sing 338 n n C13 C14 RET doub 339 e n C13 C20 RET sing 340 n n C14 C15 RET sing 341 n n C14 H14 RET sing 342 n n C15 O1 RET doub 343 n n C15 H15 RET sing 344 n n C16 H161 RET sing 345 n n C16 H162 RET sing 346 n n C16 H163 RET sing 347 n n C17 H171 RET sing 348 n n C17 H172 RET sing 349 n n C17 H173 RET sing 350 n n C18 H181 RET sing 351 n n C18 H182 RET sing 352 n n C18 H183 RET sing 353 n n C19 H191 RET sing 354 n n C19 H192 RET sing 355 n n C19 H193 RET sing 356 n n C20 H201 RET sing 357 n n C20 H202 RET sing 358 n n C20 H203 RET sing 359 n n # _atom_sites.entry_id 2J4Y _atom_sites.fract_transf_matrix[1][1] 0.009149 _atom_sites.fract_transf_matrix[1][2] 0.005282 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010565 _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] 0.01287 _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 RET A 1 1296 1296 RET RET . D 3 NAG A 1 1327 1327 NAG NAG . E 2 RET B 1 1296 1296 RET RET . F 3 NAG B 1 1327 1327 NAG NAG . # 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 . . . C 2 -7.084 17.617 1.424 1 39.51 ? C1 RET 1296 A 1 HETATM 2 C C2 RET . . . C 2 -6.046 18.714 1.776 1 39.81 ? C2 RET 1296 A 1 HETATM 3 C C3 RET . . . C 2 -4.627 18.391 1.343 1 41.17 ? C3 RET 1296 A 1 HETATM 4 C C4 RET . . . C 2 -4.137 16.992 1.823 1 41.2 ? C4 RET 1296 A 1 HETATM 5 C C5 RET . . . C 2 -5.224 15.898 1.876 1 40.1 ? C5 RET 1296 A 1 HETATM 6 C C6 RET . . . C 2 -6.544 16.161 1.666 1 39.04 ? C6 RET 1296 A 1 HETATM 7 C C7 RET . . . C 2 -7.594 15.105 1.663 1 37.24 ? C7 RET 1296 A 1 HETATM 8 C C8 RET . . . C 2 -7.677 14.164 0.745 1 36.16 ? C8 RET 1296 A 1 HETATM 9 C C9 RET . . . C 2 -8.668 13.14 0.56 1 36.13 ? C9 RET 1296 A 1 HETATM 10 C C10 RET . . . C 2 -8.409 12.341 -0.474 1 36.27 ? C10 RET 1296 A 1 HETATM 11 C C11 RET . . . C 2 -9.197 11.251 -0.967 1 38.06 ? C11 RET 1296 A 1 HETATM 12 C C12 RET . . . C 2 -8.946 10.423 -2.011 1 39.06 ? C12 RET 1296 A 1 HETATM 13 C C13 RET . . . C 2 -7.821 10.28 -2.97 1 38.39 ? C13 RET 1296 A 1 HETATM 14 C C14 RET . . . C 2 -7.955 9.264 -3.866 1 37.78 ? C14 RET 1296 A 1 HETATM 15 C C15 RET . . . C 2 -6.979 8.951 -4.871 1 38.33 ? C15 RET 1296 A 1 HETATM 16 C C16 RET . . . C 2 -8.314 17.926 2.283 1 40.09 ? C16 RET 1296 A 1 HETATM 17 C C17 RET . . . C 2 -7.571 17.767 -0.023 1 40.39 ? C17 RET 1296 A 1 HETATM 18 C C18 RET . . . C 2 -4.611 14.552 2.187 1 40.63 ? C18 RET 1296 A 1 HETATM 19 C C19 RET . . . C 2 -9.872 13.068 1.502 1 35.06 ? C19 RET 1296 A 1 HETATM 20 C C20 RET . . . C 2 -6.579 11.165 -2.982 1 36.42 ? C20 RET 1296 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 20 #