data_4ZDK # _model_server_result.job_id UVBFKdtEBUJXvBS_l9ZlgQ _model_server_result.datetime_utc '2024-10-28 14:23:31' _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 4zdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 4ZDK # _exptl.entry_id 4ZDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.156 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-OXO-L-NORLEUCINE _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 4ZDK _cell.length_a 121.732 _cell.length_b 194.724 _cell.length_c 207.457 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,G,H,I,J 1 1 A,C,D,E,F 1 2 B,G,H,I,J 1 4 A,C,D,E,F 1 6 A,C,D,E,F 2 1,5 B,G,H,I,J 2 3,6 # 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' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 60.866 -97.362 0 3 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -60.866 -97.362 0 4 'crystal symmetry operation' 6_645 -x+1,-y-1/2,z -1 0 0 0 -1 0 0 0 1 121.732 -97.362 0 5 'crystal symmetry operation' 6_545 -x,-y-1/2,z -1 0 0 0 -1 0 0 0 1 0 -97.362 0 6 'crystal symmetry operation' 7_555 -x+1/2,y,-z -1 0 0 0 1 0 0 0 -1 60.866 0 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 G 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 SG CYS 393 A CYS 393 1_555 C CE ONL . A ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B SG CYS 393 B CYS 393 1_555 G CE ONL . B ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc1 A OD1 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc3 A OE1 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc4 A OE2 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc5 D O3G ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc6 D O1B ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc7 B OD2 ASP 78 B ASP 78 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 B OE2 GLU 152 B GLU 152 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc9 H O1B ACP . B ACP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C6 H11 N O3' _chem_comp.formula_weight 145.156 _chem_comp.id ONL _chem_comp.mon_nstd_flag . _chem_comp.name 5-OXO-L-NORLEUCINE _chem_comp.type 'l-peptide linking' _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 N CA ONL sing 286 n n N H ONL sing 287 n n N H2 ONL sing 288 n n CA C ONL sing 289 n n CA CB ONL sing 290 n n CA HA ONL sing 291 n n C O ONL doub 292 n n C OXT ONL sing 293 n n OXT HXT ONL sing 294 n n CB CG ONL sing 295 n n CB HB1 ONL sing 296 n n CB HB2 ONL sing 297 n n CG CD ONL sing 298 n n CG HG1 ONL sing 299 n n CG HG2 ONL sing 300 n n CD OD ONL doub 301 n n CD CE ONL sing 302 n n CE HE1 ONL sing 303 n n CE HE2 ONL sing 304 n n CE HE3 ONL sing 305 n n # _atom_sites.entry_id 4ZDK _atom_sites.fract_transf_matrix[1][1] 0.008215 _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] 0.005135 _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] 0.00482 _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 ONL A 1 601 601 ONL ONL . D 3 ACP A 1 602 1 ACP ACP . E 4 UTP A 1 603 3 UTP UTP . F 5 MG A 1 604 5 MG MG . G 2 ONL B 1 601 601 ONL ONL . H 3 ACP B 1 602 2 ACP ACP . I 4 UTP B 1 603 4 UTP UTP . J 5 MG B 1 604 6 MG MG . # 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 N N ONL . . . G 2 53.902 -25.27 -33.258 1 160.15 ? N ONL 601 B 1 HETATM 2 C CA ONL . . . G 2 54.523 -23.988 -33.647 1 159.83 ? CA ONL 601 B 1 HETATM 3 C C ONL . . . G 2 55.281 -24.071 -34.986 1 163.48 ? C ONL 601 B 1 HETATM 4 O O ONL . . . G 2 55.433 -22.886 -35.528 1 163.47 ? O ONL 601 B 1 HETATM 5 O OXT ONL . . . G 2 55.709 -25.107 -35.466 1 166.25 ? OXT ONL 601 B 1 HETATM 6 C CB ONL . . . G 2 55.559 -23.53 -32.622 1 157.04 ? CB ONL 601 B 1 HETATM 7 C CG ONL . . . G 2 55.021 -22.337 -31.837 1 154.04 ? CG ONL 601 B 1 HETATM 8 C CD ONL . . . G 2 56.067 -21.474 -31.189 1 152.17 ? CD ONL 601 B 1 HETATM 9 O OD ONL . . . G 2 55.759 -20.55 -30.479 1 151.66 ? OD ONL 601 B 1 HETATM 10 C CE ONL . . . G 2 57.503 -21.814 -31.419 1 150.93 ? CE ONL 601 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #