data_7NQ4 # _model_server_result.job_id j2Qlz96iMWfCcZrEeJlBkA _model_server_result.datetime_utc '2025-03-20 05:19:25' _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 7nq4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 7NQ4 # _exptl.entry_id 7NQ4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.138 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-DEAZAGUANINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.935 _cell.angle_gamma 90 _cell.entry_id 7NQ4 _cell.length_a 161.84 _cell.length_b 56.96 _cell.length_c 102.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NQ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A SG CYS 319 A CYS 317 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc2 A SG CYS 321 A CYS 319 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc3 A SG CYS 324 A CYS 322 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc4 A ND1 HIS 350 A HIS 348 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc5 B SG CYS 351 B CYS 351 1_555 F ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc6 B SG CYS 353 B CYS 353 1_555 F ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc7 B SG CYS 356 B CYS 356 1_555 F ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc8 B ND1 HIS 382 B HIS 382 1_555 F ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? hydrog WATSON-CRICK hydrog1 C N1 G 2 C G 26 1_555 C N3 C 20 C C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N2 G 2 C G 26 1_555 C O2 C 20 C C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O6 G 2 C G 26 1_555 C N4 C 20 C C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N3 C 3 C C 27 1_555 C N1 G 19 C G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N4 C 3 C C 27 1_555 C O6 G 19 C G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C O2 C 3 C C 27 1_555 C N2 G 19 C G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N1 A 4 C A 28 1_555 C N3 U 18 C U 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N6 A 4 C A 28 1_555 C O4 U 18 C U 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N3 C 5 C C 29 1_555 C N1 G 17 C G 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N4 C 5 C C 29 1_555 C O6 G 17 C G 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C O2 C 5 C C 29 1_555 C N2 G 17 C G 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N1 G 6 C G 30 1_555 C N3 C 16 C C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N2 G 6 C G 30 1_555 C O2 C 16 C C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C O6 G 6 C G 30 1_555 C N4 C 16 C C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N1 G 7 C G 31 1_555 C N3 C 15 C C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N2 G 7 C G 31 1_555 C O2 C 15 C C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O6 G 7 C G 31 1_555 C N4 C 15 C C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H6 N4 O' _chem_comp.formula_weight 150.138 _chem_comp.id 9DG _chem_comp.mon_nstd_flag . _chem_comp.name 9-DEAZAGUANINE _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 C9 C8 9DG doub 1 n y C9 C4 9DG sing 2 n y C9 H9 9DG sing 3 n n C8 N7 9DG sing 4 n y C8 H8 9DG sing 5 n n N7 C5 9DG sing 6 n y N7 HN7 9DG sing 7 n n C5 C6 9DG sing 8 n n C5 C4 9DG doub 9 n y C6 O6 9DG doub 10 n n C6 N1 9DG sing 11 n n N1 C2 9DG sing 12 n n N1 HN1 9DG sing 13 n n C2 N2 9DG sing 14 n n C2 N3 9DG doub 15 n n N2 HN21 9DG sing 16 n n N2 HN22 9DG sing 17 n n N3 C4 9DG sing 18 n n # _atom_sites.entry_id 7NQ4 _atom_sites.fract_transf_matrix[1][1] 0.006179 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004316 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017556 _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] 0.011847 _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 D 4 ZN A 1 501 501 ZN ZN . E 5 9DG A 1 502 601 9DG 9DG . F 4 ZN B 1 501 501 ZN ZN . G 6 HOH A 1 601 3 HOH HOH . H 6 HOH B 1 601 5 HOH HOH . H 6 HOH B 2 602 8 HOH HOH . H 6 HOH B 3 603 4 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 C9 9DG . . . E 5 22.834 -25.855 37.674 1 60.4 ? C9 9DG 502 A 1 HETATM 2 C C8 9DG . . . E 5 22.809 -24.55 38.063 1 62.47 ? C8 9DG 502 A 1 HETATM 3 N N7 9DG . . . E 5 22.624 -24.488 39.417 1 64.47 ? N7 9DG 502 A 1 HETATM 4 C C5 9DG . . . E 5 22.534 -25.772 39.897 1 65.13 ? C5 9DG 502 A 1 HETATM 5 C C6 9DG . . . E 5 22.34 -26.292 41.215 1 67.79 ? C6 9DG 502 A 1 HETATM 6 O O6 9DG . . . E 5 22.218 -25.635 42.255 1 69.71 ? O6 9DG 502 A 1 HETATM 7 N N1 9DG . . . E 5 22.286 -27.681 41.253 1 66.03 ? N1 9DG 502 A 1 HETATM 8 C C2 9DG . . . E 5 22.415 -28.485 40.148 1 64.69 ? C2 9DG 502 A 1 HETATM 9 N N2 9DG . . . E 5 22.353 -29.806 40.356 1 65.58 ? N2 9DG 502 A 1 HETATM 10 N N3 9DG . . . E 5 22.611 -27.997 38.925 1 61.65 ? N3 9DG 502 A 1 HETATM 11 C C4 9DG . . . E 5 22.661 -26.634 38.797 1 61.9 ? C4 9DG 502 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 11 #