data_8JNR # _model_server_result.job_id ViZrB-W5BAoIX0-tFEfeDw _model_server_result.datetime_utc '2024-11-26 12:17:41' _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 8jnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1001}' # _entry.id 8JNR # _exptl.entry_id 8JNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.086 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OXALYLGLYCINE _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 113.07 _cell.angle_gamma 90 _cell.entry_id 8JNR _cell.length_a 108.615 _cell.length_b 142.171 _cell.length_c 130.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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 ? 5 O N N ? 5 R 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 G SG CYS 22 G CYS 22 1_555 G SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 G SG CYS 140 G CYS 140 1_555 G SG CYS 196 G CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf4 H SG CYS 140 H CYS 140 1_555 H SG CYS 196 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 I SG CYS 22 I CYS 22 1_555 I SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 I SG CYS 140 I CYS 140 1_555 I SG CYS 196 I CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 J SG CYS 140 J CYS 140 1_555 J SG CYS 196 J CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 K SG CYS 24 K CYS 24 1_555 K SG CYS 89 K CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf10 K SG CYS 137 K CYS 137 1_555 K SG CYS 197 K CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 L SG CYS 24 L CYS 24 1_555 L SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf12 L SG CYS 137 L CYS 137 1_555 L SG CYS 197 L CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 M SG CYS 24 M CYS 24 1_555 M SG CYS 89 M CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 M SG CYS 137 M CYS 137 1_555 M SG CYS 197 M CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 N SG CYS 24 N CYS 24 1_555 N SG CYS 89 N CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf16 N SG CYS 137 N CYS 137 1_555 N SG CYS 197 N CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 B O3' DT 1 B DT 4 1_555 B P ME6 2 B ME6 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.543 ? covale ? covale2 B O3' ME6 2 B ME6 5 1_555 B P DT 3 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.53 ? covale ? covale3 F O3' ME6 2 F ME6 5 1_555 F P DT 3 F DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.682 ? metalc ? metalc1 A NE2 HIS 143 A HIS 191 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A OD2 ASP 145 A ASP 193 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 A NE2 HIS 209 A HIS 257 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc4 O O1 OGA . A OGA 1001 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc5 O O2' OGA . A OGA 1001 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc6 C NE2 HIS 143 C HIS 191 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc7 C OD1 ASP 145 C ASP 193 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc8 C NE2 HIS 209 C HIS 257 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc9 D NE2 HIS 143 D HIS 191 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc10 D OD2 ASP 145 D ASP 193 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc11 D NE2 HIS 209 D HIS 257 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc12 R O2 OGA . D OGA 1001 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc13 R O2' OGA . D OGA 1001 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc14 E NE2 HIS 143 E HIS 191 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc15 E OD2 ASP 145 E ASP 193 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc16 E NE2 HIS 209 E HIS 257 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? # _chem_comp.formula 'C4 H5 N O5' _chem_comp.formula_weight 147.086 _chem_comp.id OGA _chem_comp.mon_nstd_flag . _chem_comp.name N-OXALYLGLYCINE _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 OGA sing 311 n n C1 O1 OGA doub 312 n n C1 O2 OGA sing 313 n n C2 O2' OGA doub 314 n n C2 N1 OGA sing 315 n n C4 C5 OGA sing 316 n n C4 N1 OGA sing 317 n n C4 H4C1 OGA sing 318 n n C4 H4C2 OGA sing 319 n n C5 O3 OGA sing 320 n n C5 O4 OGA doub 321 n n O2 H2 OGA sing 322 n n O3 H3 OGA sing 323 n n N1 H1 OGA sing 324 n n # _atom_sites.entry_id 8JNR _atom_sites.fract_transf_matrix[1][1] 0.009207 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003922 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007034 _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] 0.008354 _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 O 5 OGA A 1 1001 1001 OGA OGA . P 6 MN A 1 1002 1002 MN MN . Q 6 MN C 1 1001 1001 MN MN . R 5 OGA D 1 1001 1001 OGA OGA . S 6 MN D 1 1002 1002 MN MN . T 7 ME6 D 1 1003 1003 ME6 ME6 . U 6 MN E 1 1001 1001 MN MN . # 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 OGA . . . R 5 19.562 -13.737 44.732 1 80.16 ? C1 OGA 1001 D 1 HETATM 2 C C2 OGA . . . R 5 18.574 -14.716 45.367 1 73.9 ? C2 OGA 1001 D 1 HETATM 3 C C4 OGA . . . R 5 17.11 -16.763 45.16 1 60.26 ? C4 OGA 1001 D 1 HETATM 4 C C5 OGA . . . R 5 17.038 -17.983 44.259 1 64.73 ? C5 OGA 1001 D 1 HETATM 5 O O1 OGA . . . R 5 20.027 -13.952 43.585 1 87.01 ? O1 OGA 1001 D 1 HETATM 6 O O2 OGA . . . R 5 19.929 -12.71 45.355 1 71.18 ? O2 OGA 1001 D 1 HETATM 7 O O2' OGA . . . R 5 18.249 -14.576 46.497 1 74.19 ? O2' OGA 1001 D 1 HETATM 8 O O3 OGA . . . R 5 15.973 -18.646 44.218 1 60.77 ? O3 OGA 1001 D 1 HETATM 9 N N1 OGA . . . R 5 18.043 -15.813 44.583 1 63.75 ? N1 OGA 1001 D 1 HETATM 10 O O4 OGA . . . R 5 18.033 -18.329 43.564 1 68.12 ? O4 OGA 1001 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #