data_5ZMD # _model_server_result.job_id WmBeZgfWnCUbu2xQIZ9Rpg _model_server_result.datetime_utc '2024-11-27 14:38:54' _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 5zmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1002}' # _entry.id 5ZMD # _exptl.entry_id 5ZMD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.086 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OXALYLGLYCINE _entity.pdbx_number_of_molecules 4 _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 5ZMD _cell.length_a 122.736 _cell.length_b 160.033 _cell.length_c 276.756 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZMD _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 ? tetrameric 4 author_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,D,I,J,K,L,Q,R,S 1 1 E,F,G,H,M,N,O,P,T,U 2 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 J N N ? 4 L N N ? 4 N N N ? 4 P 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 41 A CYS 77 1_555 A SG CYS 356 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? disulf ? disulf2 G SG CYS 41 G CYS 77 1_555 G SG CYS 356 G CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale1 B O3' DT 3 B DT 4 1_555 B P 6MA 4 B 6MA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale2 B O3' 6MA 4 B 6MA 5 1_555 B P DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 D O3' DT 3 D DT 4 1_555 D P 6MA 4 D 6MA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale4 D O3' 6MA 4 D 6MA 5 1_555 D P DT 5 D DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale5 F O3' DT 3 F DT 4 1_555 F P 6MA 4 F 6MA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale6 F O3' 6MA 4 F 6MA 5 1_555 F P DT 5 F DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale7 H O3' DT 3 H DT 4 1_555 H P 6MA 4 H 6MA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale8 H O3' 6MA 4 H 6MA 5 1_555 H P DT 5 H DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 A NE2 HIS 195 A HIS 231 1_555 I MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc2 A OD1 ASP 197 A ASP 233 1_555 I MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc3 A OD2 ASP 197 A ASP 233 1_555 I MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc4 A NE2 HIS 271 A HIS 307 1_555 I MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc5 I MN MN . A MN 1001 1_555 J O2' OGA . A OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc6 I MN MN . A MN 1001 1_555 J O1 OGA . A OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc7 C NE2 HIS 195 C HIS 231 1_555 K MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc8 C OD1 ASP 197 C ASP 233 1_555 K MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc9 C NE2 HIS 271 C HIS 307 1_555 K MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc10 K MN MN . C MN 1001 1_555 L O2 OGA . C OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc11 E NE2 HIS 195 E HIS 231 1_555 M MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc12 E OD1 ASP 197 E ASP 233 1_555 M MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc13 E NE2 HIS 271 E HIS 307 1_555 M MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc14 M MN MN . E MN 1001 1_555 N O2 OGA . E OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc15 M MN MN . E MN 1001 1_555 N O2' OGA . E OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc16 G NE2 HIS 195 G HIS 231 1_555 O MN MN . G MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc17 G OD1 ASP 197 G ASP 233 1_555 O MN MN . G MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? metalc ? metalc18 G NE2 HIS 271 G HIS 307 1_555 O MN MN . G MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc19 O MN MN . G MN 1001 1_555 P O1 OGA . G OGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? hydrog 'DC-DG PAIR' hydrog1 B N4 DC 8 B DC 9 1_555 D O6 DG 9 D DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog2 B O6 DG 9 B DG 10 1_555 D N4 DC 8 D DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog3 F N4 DC 8 F DC 9 1_555 H O6 DG 9 H DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog4 F O6 DG 9 F DG 10 1_555 H N4 DC 8 H DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 427 n n C1 O1 OGA doub 428 n n C1 O2 OGA sing 429 n n C2 O2' OGA doub 430 n n C2 N1 OGA sing 431 n n C4 C5 OGA sing 432 n n C4 N1 OGA sing 433 n n C4 H4C1 OGA sing 434 n n C4 H4C2 OGA sing 435 n n C5 O3 OGA sing 436 n n C5 O4 OGA doub 437 n n O2 H2 OGA sing 438 n n O3 H3 OGA sing 439 n n N1 H1 OGA sing 440 n n # _atom_sites.entry_id 5ZMD _atom_sites.fract_transf_matrix[1][1] 0.008148 _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] 0.006249 _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] 0.003613 _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 I 3 MN A 1 1001 1001 MN MN . J 4 OGA A 1 1002 1002 OGA OGA . K 3 MN C 1 1001 1001 MN MN . L 4 OGA C 1 1002 1002 OGA OGA . M 3 MN E 1 1001 1001 MN MN . N 4 OGA E 1 1002 1002 OGA OGA . O 3 MN G 1 1001 1001 MN MN . P 4 OGA G 1 1002 1002 OGA OGA . Q 5 HOH A 1 1101 1101 HOH HOH . Q 5 HOH A 2 1102 1102 HOH HOH . Q 5 HOH A 3 1103 1103 HOH HOH . Q 5 HOH A 4 1104 1104 HOH HOH . Q 5 HOH A 5 1105 1105 HOH HOH . Q 5 HOH A 6 1106 1106 HOH HOH . Q 5 HOH A 7 1107 1107 HOH HOH . Q 5 HOH A 8 1108 1108 HOH HOH . Q 5 HOH A 9 1109 1109 HOH HOH . Q 5 HOH A 10 1110 1110 HOH HOH . R 5 HOH C 1 1101 1101 HOH HOH . R 5 HOH C 2 1102 1102 HOH HOH . R 5 HOH C 3 1103 1103 HOH HOH . S 5 HOH D 1 101 101 HOH HOH . S 5 HOH D 2 102 102 HOH HOH . T 5 HOH E 1 1101 1101 HOH HOH . U 5 HOH G 1 1101 1101 HOH HOH . U 5 HOH G 2 1102 1102 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 OGA . . . N 4 45.681 -23.941 -48.384 1 24.34 ? C1 OGA 1002 E 1 HETATM 2 C C2 OGA . . . N 4 44.715 -24.993 -48.085 1 18.4 ? C2 OGA 1002 E 1 HETATM 3 C C4 OGA . . . N 4 43.243 -26.927 -48.75 1 23.92 ? C4 OGA 1002 E 1 HETATM 4 C C5 OGA . . . N 4 43.017 -28.021 -49.786 1 22.62 ? C5 OGA 1002 E 1 HETATM 5 O O1 OGA . . . N 4 46.45 -24.053 -49.372 1 29.63 ? O1 OGA 1002 E 1 HETATM 6 O O2 OGA . . . N 4 45.717 -22.938 -47.63 1 23.91 ? O2 OGA 1002 E 1 HETATM 7 O O2' OGA . . . N 4 44.104 -24.942 -47.02 1 17.14 ? O2' OGA 1002 E 1 HETATM 8 O O3 OGA . . . N 4 41.948 -28.662 -49.681 1 24.89 ? O3 OGA 1002 E 1 HETATM 9 N N1 OGA . . . N 4 44.499 -26.124 -49.08 1 20.72 ? N1 OGA 1002 E 1 HETATM 10 O O4 OGA . . . N 4 43.889 -28.27 -50.654 1 14.73 ? O4 OGA 1002 E 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 10 #