data_178D # _entry.id 178D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 178D pdb_0000178d 10.2210/pdb178d/pdb RCSB BDLB56 ? ? WWPDB D_1000170173 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1994-10-04 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 178D _pdbx_database_status.recvd_initial_deposition_date 1994-05-19 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'McAuley-Hecht, K.E.' 1 'Leonard, G.A.' 2 'Gibson, N.J.' 3 'Thomson, J.B.' 4 'Watson, W.P.' 5 'Hunter, W.N.' 6 'Brown, T.' 7 # _citation.id primary _citation.title 'Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs.' _citation.journal_abbrev Biochemistry _citation.journal_volume 33 _citation.page_first 10266 _citation.page_last 10270 _citation.year 1994 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8068665 _citation.pdbx_database_id_DOI 10.1021/bi00200a006 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'McAuley-Hecht, K.E.' 1 ? primary 'Leonard, G.A.' 2 ? primary 'Gibson, N.J.' 3 ? primary 'Thomson, J.B.' 4 ? primary 'Watson, W.P.' 5 ? primary 'Hunter, W.N.' 6 ? primary 'Brown, T.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3') ; 3703.417 2 ? ? ? ? 2 water nat water 18.015 72 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DA)(DA)(DA)(DT)(DT)(8OG)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCAAATTGGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DA n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 8OG n 1 10 DG n 1 11 DC n 1 12 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 8OG 'DNA linking' n "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" 'C10 H14 N5 O8 P' 363.221 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 8OG 9 9 9 8OG +G A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DA 4 16 16 DA A B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 8OG 9 21 21 8OG +G B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_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_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 26 26 HOH HOH A . C 2 HOH 2 28 28 HOH HOH A . C 2 HOH 3 29 29 HOH HOH A . C 2 HOH 4 31 31 HOH HOH A . C 2 HOH 5 33 33 HOH HOH A . C 2 HOH 6 34 34 HOH HOH A . C 2 HOH 7 35 35 HOH HOH A . C 2 HOH 8 37 37 HOH HOH A . C 2 HOH 9 38 38 HOH HOH A . C 2 HOH 10 39 39 HOH HOH A . C 2 HOH 11 41 41 HOH HOH A . C 2 HOH 12 44 44 HOH HOH A . C 2 HOH 13 46 46 HOH HOH A . C 2 HOH 14 48 48 HOH HOH A . C 2 HOH 15 49 49 HOH HOH A . C 2 HOH 16 50 50 HOH HOH A . C 2 HOH 17 52 52 HOH HOH A . C 2 HOH 18 53 53 HOH HOH A . C 2 HOH 19 54 54 HOH HOH A . C 2 HOH 20 55 55 HOH HOH A . C 2 HOH 21 56 56 HOH HOH A . C 2 HOH 22 57 57 HOH HOH A . C 2 HOH 23 58 58 HOH HOH A . C 2 HOH 24 59 59 HOH HOH A . C 2 HOH 25 60 60 HOH HOH A . C 2 HOH 26 61 61 HOH HOH A . C 2 HOH 27 65 65 HOH HOH A . C 2 HOH 28 66 66 HOH HOH A . C 2 HOH 29 67 67 HOH HOH A . C 2 HOH 30 70 70 HOH HOH A . C 2 HOH 31 71 71 HOH HOH A . C 2 HOH 32 72 72 HOH HOH A . C 2 HOH 33 80 80 HOH HOH A . C 2 HOH 34 82 82 HOH HOH A . C 2 HOH 35 84 84 HOH HOH A . C 2 HOH 36 85 85 HOH HOH A . C 2 HOH 37 86 86 HOH HOH A . C 2 HOH 38 90 90 HOH HOH A . C 2 HOH 39 92 92 HOH HOH A . C 2 HOH 40 96 96 HOH HOH A . D 2 HOH 1 25 25 HOH HOH B . D 2 HOH 2 27 27 HOH HOH B . D 2 HOH 3 30 30 HOH HOH B . D 2 HOH 4 32 32 HOH HOH B . D 2 HOH 5 36 36 HOH HOH B . D 2 HOH 6 40 40 HOH HOH B . D 2 HOH 7 42 42 HOH HOH B . D 2 HOH 8 43 43 HOH HOH B . D 2 HOH 9 45 45 HOH HOH B . D 2 HOH 10 47 47 HOH HOH B . D 2 HOH 11 51 51 HOH HOH B . D 2 HOH 12 62 62 HOH HOH B . D 2 HOH 13 63 63 HOH HOH B . D 2 HOH 14 64 64 HOH HOH B . D 2 HOH 15 68 68 HOH HOH B . D 2 HOH 16 69 69 HOH HOH B . D 2 HOH 17 73 73 HOH HOH B . D 2 HOH 18 74 74 HOH HOH B . D 2 HOH 19 75 75 HOH HOH B . D 2 HOH 20 76 76 HOH HOH B . D 2 HOH 21 77 77 HOH HOH B . D 2 HOH 22 78 78 HOH HOH B . D 2 HOH 23 79 79 HOH HOH B . D 2 HOH 24 81 81 HOH HOH B . D 2 HOH 25 83 83 HOH HOH B . D 2 HOH 26 87 87 HOH HOH B . D 2 HOH 27 88 88 HOH HOH B . D 2 HOH 28 89 89 HOH HOH B . D 2 HOH 29 91 91 HOH HOH B . D 2 HOH 30 93 93 HOH HOH B . D 2 HOH 31 94 94 HOH HOH B . D 2 HOH 32 95 95 HOH HOH B . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 178D _cell.length_a 24.670 _cell.length_b 40.490 _cell.length_c 65.140 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 178D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 178D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.99 _exptl_crystal.density_Matthews 2.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 SPERMINE_HCL ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 178D _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.500 _reflns.number_obs 1965 _reflns.number_all 9923 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 178D _refine.ls_number_reflns_obs 1843 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 2.500 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.168 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 490 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 72 _refine_hist.number_atoms_total 564 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function n_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it 2.445 2.445 ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it 3.415 3.415 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it 4.496 4.496 ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d 0.006 0.006 ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d 0.014 0.014 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.005 0.005 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d 0.010 0.010 ? ? 'X-RAY DIFFRACTION' ? n_plane_restr 0.005 0.005 ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr 0.245 0.245 ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd 0.070 0.070 ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd 0.175 0.175 ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 178D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 178D _struct.title 'CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANINE.ADENINE BASE-PAIRS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 178D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, MODIFIED, MISMATCHED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 178D _struct_ref.pdbx_db_accession 178D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 178D A 1 ? 12 ? 178D 1 ? 12 ? 1 12 2 1 178D B 1 ? 12 ? 178D 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_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_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DT 8 "O3'" ? ? ? 1_555 A 8OG 9 P ? ? A DT 8 A 8OG 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? A 8OG 9 "O3'" ? ? ? 1_555 A DG 10 P ? ? A 8OG 9 A DG 10 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale3 covale both ? B DT 8 "O3'" ? ? ? 1_555 B 8OG 9 P ? ? B DT 20 B 8OG 21 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale both ? B 8OG 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B 8OG 21 B DG 22 1_555 ? ? ? ? ? ? ? 1.595 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B 8OG 9 O6 ? ? A DC 3 B 8OG 21 1_555 ? ? ? ? ? ? 'DC-8OG PAIR' ? ? ? hydrog8 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B 8OG 9 O6 ? ? A DA 4 B 8OG 21 1_555 ? ? ? ? ? ? 'DA-8OG MISPAIR' ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 8OG 9 O6 ? ? ? 1_555 B DA 4 N6 ? ? A 8OG 9 B DA 16 1_555 ? ? ? ? ? ? '8OG-DA MISPAIR' ? ? ? hydrog21 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 96.97 102.40 -5.43 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.24 108.30 2.94 0.30 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 110.94 108.30 2.64 0.30 N 4 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 114.70 111.50 3.20 0.50 N 5 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.21 108.30 1.91 0.30 N 6 1 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 126.25 129.30 -3.05 0.50 N 7 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 110.49 108.30 2.19 0.30 N 8 1 N1 A DA 5 ? ? C2 A DA 5 ? ? N3 A DA 5 ? ? 126.19 129.30 -3.11 0.50 N 9 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 125.88 129.30 -3.42 0.50 N 10 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 123.01 127.20 -4.19 0.60 N 11 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 112.09 108.30 3.79 0.30 N 12 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 122.75 127.20 -4.45 0.60 N 13 1 N3 A DT 8 ? ? C4 A DT 8 ? ? C5 A DT 8 ? ? 118.90 115.20 3.70 0.60 N 14 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 117.27 108.30 8.97 0.30 N 15 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 114.63 111.50 3.13 0.50 N 16 1 C5 A DG 12 ? ? C6 A DG 12 ? ? N1 A DG 12 ? ? 114.93 111.50 3.43 0.50 N 17 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 110.42 108.30 2.12 0.30 N 18 1 C5 B DG 14 ? ? C6 B DG 14 ? ? N1 B DG 14 ? ? 114.52 111.50 3.02 0.50 N 19 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 110.78 108.30 2.48 0.30 N 20 1 "O4'" B DA 16 ? ? "C1'" B DA 16 ? ? N9 B DA 16 ? ? 110.17 108.30 1.87 0.30 N 21 1 N1 B DA 16 ? ? C2 B DA 16 ? ? N3 B DA 16 ? ? 126.29 129.30 -3.01 0.50 N 22 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 110.19 108.30 1.89 0.30 N 23 1 N1 B DA 17 ? ? C2 B DA 17 ? ? N3 B DA 17 ? ? 126.12 129.30 -3.18 0.50 N 24 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 111.34 108.30 3.04 0.30 N 25 1 C6 B DA 18 ? ? N1 B DA 18 ? ? C2 B DA 18 ? ? 122.57 118.60 3.97 0.60 N 26 1 N1 B DA 18 ? ? C2 B DA 18 ? ? N3 B DA 18 ? ? 125.80 129.30 -3.50 0.50 N 27 1 C5 B DA 18 ? ? C6 B DA 18 ? ? N1 B DA 18 ? ? 114.53 117.70 -3.17 0.50 N 28 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 111.15 108.30 2.85 0.30 N 29 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 122.92 127.20 -4.28 0.60 N 30 1 C2 B DT 20 ? ? N3 B DT 20 ? ? C4 B DT 20 ? ? 122.62 127.20 -4.58 0.60 N 31 1 N3 B DT 20 ? ? C4 B DT 20 ? ? C5 B DT 20 ? ? 119.06 115.20 3.86 0.60 N 32 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 111.70 108.30 3.40 0.30 N 33 1 C5 B DG 22 ? ? C6 B DG 22 ? ? N1 B DG 22 ? ? 114.61 111.50 3.11 0.50 N 34 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 111.19 108.30 2.89 0.30 N 35 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 111.19 108.30 2.89 0.30 N 36 1 C5 B DG 24 ? ? C6 B DG 24 ? ? N1 B DG 24 ? ? 114.57 111.50 3.07 0.50 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 8OG 9 A 8OG 9 ? DG ? 2 B 8OG 9 B 8OG 21 ? DG ? # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 8OG OP3 O N N 1 8OG P P N N 2 8OG OP1 O N N 3 8OG OP2 O N N 4 8OG "O5'" O N N 5 8OG "C5'" C N N 6 8OG "C4'" C N R 7 8OG "O4'" O N N 8 8OG "C3'" C N S 9 8OG "O3'" O N N 10 8OG "C2'" C N N 11 8OG "C1'" C N R 12 8OG N9 N N N 13 8OG C8 C N N 14 8OG N7 N N N 15 8OG C5 C N N 16 8OG C6 C N N 17 8OG O6 O N N 18 8OG N1 N N N 19 8OG C2 C N N 20 8OG N2 N N N 21 8OG N3 N N N 22 8OG C4 C N N 23 8OG O8 O N N 24 8OG HOP3 H N N 25 8OG HOP2 H N N 26 8OG "H5'" H N N 27 8OG "H5''" H N N 28 8OG "H4'" H N N 29 8OG "H3'" H N N 30 8OG "HO3'" H N N 31 8OG "H2'" H N N 32 8OG "H2''" H N N 33 8OG "H1'" H N N 34 8OG H7 H N N 35 8OG H1 H N N 36 8OG H21 H N N 37 8OG H22 H N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DT OP3 O N N 146 DT P P N N 147 DT OP1 O N N 148 DT OP2 O N N 149 DT "O5'" O N N 150 DT "C5'" C N N 151 DT "C4'" C N R 152 DT "O4'" O N N 153 DT "C3'" C N S 154 DT "O3'" O N N 155 DT "C2'" C N N 156 DT "C1'" C N R 157 DT N1 N N N 158 DT C2 C N N 159 DT O2 O N N 160 DT N3 N N N 161 DT C4 C N N 162 DT O4 O N N 163 DT C5 C N N 164 DT C7 C N N 165 DT C6 C N N 166 DT HOP3 H N N 167 DT HOP2 H N N 168 DT "H5'" H N N 169 DT "H5''" H N N 170 DT "H4'" H N N 171 DT "H3'" H N N 172 DT "HO3'" H N N 173 DT "H2'" H N N 174 DT "H2''" H N N 175 DT "H1'" H N N 176 DT H3 H N N 177 DT H71 H N N 178 DT H72 H N N 179 DT H73 H N N 180 DT H6 H N N 181 HOH O O N N 182 HOH H1 H N N 183 HOH H2 H N N 184 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 8OG OP3 P sing N N 1 8OG OP3 HOP3 sing N N 2 8OG P OP1 doub N N 3 8OG P OP2 sing N N 4 8OG P "O5'" sing N N 5 8OG OP2 HOP2 sing N N 6 8OG "O5'" "C5'" sing N N 7 8OG "C5'" "C4'" sing N N 8 8OG "C5'" "H5'" sing N N 9 8OG "C5'" "H5''" sing N N 10 8OG "C4'" "O4'" sing N N 11 8OG "C4'" "C3'" sing N N 12 8OG "C4'" "H4'" sing N N 13 8OG "O4'" "C1'" sing N N 14 8OG "C3'" "O3'" sing N N 15 8OG "C3'" "C2'" sing N N 16 8OG "C3'" "H3'" sing N N 17 8OG "O3'" "HO3'" sing N N 18 8OG "C2'" "C1'" sing N N 19 8OG "C2'" "H2'" sing N N 20 8OG "C2'" "H2''" sing N N 21 8OG "C1'" N9 sing N N 22 8OG "C1'" "H1'" sing N N 23 8OG N9 C8 sing N N 24 8OG N9 C4 sing N N 25 8OG C8 N7 sing N N 26 8OG C8 O8 doub N N 27 8OG N7 C5 sing N N 28 8OG N7 H7 sing N N 29 8OG C5 C6 sing N N 30 8OG C5 C4 doub N N 31 8OG C6 O6 doub N N 32 8OG C6 N1 sing N N 33 8OG N1 C2 sing N N 34 8OG N1 H1 sing N N 35 8OG C2 N2 sing N N 36 8OG C2 N3 doub N N 37 8OG N2 H21 sing N N 38 8OG N2 H22 sing N N 39 8OG N3 C4 sing N N 40 DA OP3 P sing N N 41 DA OP3 HOP3 sing N N 42 DA P OP1 doub N N 43 DA P OP2 sing N N 44 DA P "O5'" sing N N 45 DA OP2 HOP2 sing N N 46 DA "O5'" "C5'" sing N N 47 DA "C5'" "C4'" sing N N 48 DA "C5'" "H5'" sing N N 49 DA "C5'" "H5''" sing N N 50 DA "C4'" "O4'" sing N N 51 DA "C4'" "C3'" sing N N 52 DA "C4'" "H4'" sing N N 53 DA "O4'" "C1'" sing N N 54 DA "C3'" "O3'" sing N N 55 DA "C3'" "C2'" sing N N 56 DA "C3'" "H3'" sing N N 57 DA "O3'" "HO3'" sing N N 58 DA "C2'" "C1'" sing N N 59 DA "C2'" "H2'" sing N N 60 DA "C2'" "H2''" sing N N 61 DA "C1'" N9 sing N N 62 DA "C1'" "H1'" sing N N 63 DA N9 C8 sing Y N 64 DA N9 C4 sing Y N 65 DA C8 N7 doub Y N 66 DA C8 H8 sing N N 67 DA N7 C5 sing Y N 68 DA C5 C6 sing Y N 69 DA C5 C4 doub Y N 70 DA C6 N6 sing N N 71 DA C6 N1 doub Y N 72 DA N6 H61 sing N N 73 DA N6 H62 sing N N 74 DA N1 C2 sing Y N 75 DA C2 N3 doub Y N 76 DA C2 H2 sing N N 77 DA N3 C4 sing Y N 78 DC OP3 P sing N N 79 DC OP3 HOP3 sing N N 80 DC P OP1 doub N N 81 DC P OP2 sing N N 82 DC P "O5'" sing N N 83 DC OP2 HOP2 sing N N 84 DC "O5'" "C5'" sing N N 85 DC "C5'" "C4'" sing N N 86 DC "C5'" "H5'" sing N N 87 DC "C5'" "H5''" sing N N 88 DC "C4'" "O4'" sing N N 89 DC "C4'" "C3'" sing N N 90 DC "C4'" "H4'" sing N N 91 DC "O4'" "C1'" sing N N 92 DC "C3'" "O3'" sing N N 93 DC "C3'" "C2'" sing N N 94 DC "C3'" "H3'" sing N N 95 DC "O3'" "HO3'" sing N N 96 DC "C2'" "C1'" sing N N 97 DC "C2'" "H2'" sing N N 98 DC "C2'" "H2''" sing N N 99 DC "C1'" N1 sing N N 100 DC "C1'" "H1'" sing N N 101 DC N1 C2 sing N N 102 DC N1 C6 sing N N 103 DC C2 O2 doub N N 104 DC C2 N3 sing N N 105 DC N3 C4 doub N N 106 DC C4 N4 sing N N 107 DC C4 C5 sing N N 108 DC N4 H41 sing N N 109 DC N4 H42 sing N N 110 DC C5 C6 doub N N 111 DC C5 H5 sing N N 112 DC C6 H6 sing N N 113 DG OP3 P sing N N 114 DG OP3 HOP3 sing N N 115 DG P OP1 doub N N 116 DG P OP2 sing N N 117 DG P "O5'" sing N N 118 DG OP2 HOP2 sing N N 119 DG "O5'" "C5'" sing N N 120 DG "C5'" "C4'" sing N N 121 DG "C5'" "H5'" sing N N 122 DG "C5'" "H5''" sing N N 123 DG "C4'" "O4'" sing N N 124 DG "C4'" "C3'" sing N N 125 DG "C4'" "H4'" sing N N 126 DG "O4'" "C1'" sing N N 127 DG "C3'" "O3'" sing N N 128 DG "C3'" "C2'" sing N N 129 DG "C3'" "H3'" sing N N 130 DG "O3'" "HO3'" sing N N 131 DG "C2'" "C1'" sing N N 132 DG "C2'" "H2'" sing N N 133 DG "C2'" "H2''" sing N N 134 DG "C1'" N9 sing N N 135 DG "C1'" "H1'" sing N N 136 DG N9 C8 sing Y N 137 DG N9 C4 sing Y N 138 DG C8 N7 doub Y N 139 DG C8 H8 sing N N 140 DG N7 C5 sing Y N 141 DG C5 C6 sing N N 142 DG C5 C4 doub Y N 143 DG C6 O6 doub N N 144 DG C6 N1 sing N N 145 DG N1 C2 sing N N 146 DG N1 H1 sing N N 147 DG C2 N2 sing N N 148 DG C2 N3 doub N N 149 DG N2 H21 sing N N 150 DG N2 H22 sing N N 151 DG N3 C4 sing N N 152 DT OP3 P sing N N 153 DT OP3 HOP3 sing N N 154 DT P OP1 doub N N 155 DT P OP2 sing N N 156 DT P "O5'" sing N N 157 DT OP2 HOP2 sing N N 158 DT "O5'" "C5'" sing N N 159 DT "C5'" "C4'" sing N N 160 DT "C5'" "H5'" sing N N 161 DT "C5'" "H5''" sing N N 162 DT "C4'" "O4'" sing N N 163 DT "C4'" "C3'" sing N N 164 DT "C4'" "H4'" sing N N 165 DT "O4'" "C1'" sing N N 166 DT "C3'" "O3'" sing N N 167 DT "C3'" "C2'" sing N N 168 DT "C3'" "H3'" sing N N 169 DT "O3'" "HO3'" sing N N 170 DT "C2'" "C1'" sing N N 171 DT "C2'" "H2'" sing N N 172 DT "C2'" "H2''" sing N N 173 DT "C1'" N1 sing N N 174 DT "C1'" "H1'" sing N N 175 DT N1 C2 sing N N 176 DT N1 C6 sing N N 177 DT C2 O2 doub N N 178 DT C2 N3 sing N N 179 DT N3 C4 sing N N 180 DT N3 H3 sing N N 181 DT C4 O4 doub N N 182 DT C4 C5 sing N N 183 DT C5 C7 sing N N 184 DT C5 C6 doub N N 185 DT C7 H71 sing N N 186 DT C7 H72 sing N N 187 DT C7 H73 sing N N 188 DT C6 H6 sing N N 189 HOH O H1 sing N N 190 HOH O H2 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 178D 'double helix' 178D 'b-form double helix' 178D 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.214 -0.325 -0.266 7.263 -14.618 0.167 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.263 -0.434 0.228 -0.100 -11.207 -4.706 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.166 -0.317 -0.038 -5.986 -7.394 1.206 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DA 4 1_555 B 8OG 9 1_555 -0.766 5.111 -0.026 -0.315 -20.468 -84.342 4 A_DA4:8OG21_B A 4 ? B 21 ? ? ? 1 A DA 5 1_555 B DT 8 1_555 -0.040 -0.379 -0.071 5.848 -22.838 -1.233 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.487 -0.457 0.336 5.174 -21.972 -4.569 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.080 -0.455 0.060 -0.698 -18.903 2.495 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.038 -0.520 0.499 -12.150 -26.157 -8.050 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A 8OG 9 1_555 B DA 4 1_555 0.086 -4.428 -0.188 2.612 18.588 83.556 9 A_8OG9:DA16_B A 9 ? B 16 ? ? ? 1 A DG 10 1_555 B DC 3 1_555 0.808 -0.445 0.375 4.448 -7.470 -2.601 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 -0.080 -0.454 0.469 -6.403 -18.765 -7.426 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 0.061 -0.294 0.278 1.997 5.237 0.506 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.503 0.252 3.623 -2.731 5.957 37.947 -0.445 0.383 3.646 9.078 4.161 38.488 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.903 0.245 3.587 4.085 -5.097 36.322 1.151 -0.814 3.598 -8.095 -6.488 36.885 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DA 4 1_555 B 8OG 9 1_555 0.857 -1.305 2.761 3.638 9.078 66.554 -1.471 -0.657 2.623 8.226 -3.297 67.187 3 AA_DC3DA4:8OG21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B 8OG 9 1_555 A DA 5 1_555 B DT 8 1_555 0.181 2.341 3.505 0.277 3.369 -0.177 -61.150 4.832 -2.162 -86.714 7.122 -3.385 4 AA_DA4DA5:DT208OG21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.046 -0.342 3.098 -3.509 2.364 41.338 -0.719 -0.287 3.068 3.338 4.955 41.545 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.384 -0.762 3.433 3.274 -3.695 29.509 -0.658 -0.019 3.522 -7.191 -6.371 29.910 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.715 -0.402 3.580 -2.222 1.817 36.098 -0.927 0.807 3.593 2.927 3.580 36.208 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A 8OG 9 1_555 B DA 4 1_555 0.155 -3.341 2.252 -174.914 1.652 -16.329 1.661 -1.118 0.505 -0.847 -89.635 -174.973 8 AA_DT88OG9:DA16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A 8OG 9 1_555 B DA 4 1_555 A DG 10 1_555 B DC 3 1_555 -2.904 -1.657 -0.619 139.497 -108.206 1.450 -1.406 0.709 -1.287 -55.149 -71.096 176.545 9 AA_8OG9DG10:DC15DA16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.330 0.551 3.771 -4.285 -13.816 37.156 2.654 1.383 3.485 -20.744 6.434 39.780 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 1.045 -0.087 3.283 4.210 -2.137 35.030 0.179 -1.085 3.381 -3.531 -6.955 35.337 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 178D _atom_sites.fract_transf_matrix[1][1] 0.040535 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.024697 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.015352 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_