data_1D75 # _entry.id 1D75 # _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 1D75 pdb_00001d75 10.2210/pdb1d75/pdb RCSB BDLB33 ? ? WWPDB D_1000172673 ? ? # 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 1993-01-15 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 1D75 _pdbx_database_status.recvd_initial_deposition_date 1992-05-07 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Leonard, G.A.' 1 'Guy, A.' 2 'Brown, T.' 3 'Teoule, R.' 4 'Hunter, W.N.' 5 # _citation.id primary _citation.title 'Conformation of guanine-8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG).' _citation.journal_abbrev Biochemistry _citation.journal_volume 31 _citation.page_first 8415 _citation.page_last 8420 _citation.year 1992 _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 1390625 _citation.pdbx_database_id_DOI 10.1021/bi00151a004 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Leonard, G.A.' 1 ? primary 'Guy, A.' 2 ? primary 'Brown, T.' 3 ? primary 'Teoule, R.' 4 ? primary 'Hunter, W.N.' 5 ? # 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*GP*AP*AP*TP*TP*(A38)P*GP*CP*G)-3') ; 3703.416 2 ? ? ? ? 2 water nat water 18.015 67 ? ? ? ? # _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)(DG)(DA)(DA)(DT)(DT)(A38)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTAGCG _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 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 A38 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 A38 'DNA linking' n ;8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE ; ? 'C10 H14 N5 O7 P' 347.221 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 DG 4 4 4 DG G 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 A38 9 9 9 A38 +A 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 DG 4 16 16 DG G 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 A38 9 21 21 A38 +A 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 25 25 HOH HOH A . C 2 HOH 2 26 26 HOH HOH A . C 2 HOH 3 28 28 HOH HOH A . C 2 HOH 4 31 31 HOH HOH A . C 2 HOH 5 32 32 HOH HOH A . C 2 HOH 6 33 33 HOH HOH A . C 2 HOH 7 35 35 HOH HOH A . C 2 HOH 8 36 36 HOH HOH A . C 2 HOH 9 37 37 HOH HOH A . C 2 HOH 10 38 38 HOH HOH A . C 2 HOH 11 40 40 HOH HOH A . C 2 HOH 12 41 41 HOH HOH A . C 2 HOH 13 42 42 HOH HOH A . C 2 HOH 14 43 43 HOH HOH A . C 2 HOH 15 44 44 HOH HOH A . C 2 HOH 16 46 46 HOH HOH A . C 2 HOH 17 48 48 HOH HOH A . C 2 HOH 18 50 50 HOH HOH A . C 2 HOH 19 51 51 HOH HOH A . C 2 HOH 20 52 52 HOH HOH A . C 2 HOH 21 54 54 HOH HOH A . C 2 HOH 22 55 55 HOH HOH A . C 2 HOH 23 56 56 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 62 62 HOH HOH A . C 2 HOH 28 63 63 HOH HOH A . C 2 HOH 29 64 64 HOH HOH A . C 2 HOH 30 65 65 HOH HOH A . C 2 HOH 31 72 72 HOH HOH A . C 2 HOH 32 74 74 HOH HOH A . C 2 HOH 33 77 77 HOH HOH A . C 2 HOH 34 78 78 HOH HOH A . C 2 HOH 35 79 79 HOH HOH A . C 2 HOH 36 80 80 HOH HOH A . C 2 HOH 37 84 84 HOH HOH A . C 2 HOH 38 86 86 HOH HOH A . C 2 HOH 39 87 87 HOH HOH A . C 2 HOH 40 88 88 HOH HOH A . C 2 HOH 41 89 89 HOH HOH A . C 2 HOH 42 90 90 HOH HOH A . C 2 HOH 43 91 91 HOH HOH A . D 2 HOH 1 27 27 HOH HOH B . D 2 HOH 2 29 29 HOH HOH B . D 2 HOH 3 30 30 HOH HOH B . D 2 HOH 4 34 34 HOH HOH B . D 2 HOH 5 39 39 HOH HOH B . D 2 HOH 6 45 45 HOH HOH B . D 2 HOH 7 47 47 HOH HOH B . D 2 HOH 8 49 49 HOH HOH B . D 2 HOH 9 53 53 HOH HOH B . D 2 HOH 10 57 57 HOH HOH B . D 2 HOH 11 58 58 HOH HOH B . D 2 HOH 12 66 66 HOH HOH B . D 2 HOH 13 67 67 HOH HOH B . D 2 HOH 14 68 68 HOH HOH B . D 2 HOH 15 69 69 HOH HOH B . D 2 HOH 16 70 70 HOH HOH B . D 2 HOH 17 71 71 HOH HOH B . D 2 HOH 18 73 73 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 81 81 HOH HOH B . D 2 HOH 22 82 82 HOH HOH B . D 2 HOH 23 83 83 HOH HOH B . D 2 HOH 24 85 85 HOH HOH B . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1D75 _cell.length_a 25.480 _cell.length_b 41.840 _cell.length_c 64.910 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D75 _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 # _exptl.entry_id 1D75 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.34 _exptl_crystal.density_percent_sol 47.34 _exptl_crystal.description ? # _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 7.40 _exptl_crystal_grow.pdbx_details 'pH 7.40, 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 'NA CACODYLATE' ? ? ? 1 4 1 'MG ACETATE' ? ? ? 1 5 1 SPERMINE ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 297.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'RIGAKU AFC-5' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.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 ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1D75 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 5.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 2.200 _reflns.number_obs 3485 _reflns.number_all 5624 _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.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1D75 _refine.ls_number_reflns_obs 1119 _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 7.000 _refine.ls_d_res_high 2.800 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.151 _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.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 67 _refine_hist.number_atoms_total 559 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 7.000 # 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 ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it ? ? ? ? '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 0.009 ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d 0.022 ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d 0.016 ? ? ? 'X-RAY DIFFRACTION' ? n_plane_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1D75 _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 1D75 _struct.title 'CONFORMATION OF THE GUANINE.8-OXOADENINE BASE PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(O8A)GCG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D75 _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 1D75 _struct_ref.pdbx_db_accession 1D75 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1D75 A 1 ? 12 ? 1D75 1 ? 12 ? 1 12 2 1 1D75 B 1 ? 12 ? 1D75 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 # 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 A38 9 P ? ? A DT 8 A A38 9 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale2 covale one ? A A38 9 "O3'" ? ? ? 1_555 A DG 10 P ? ? A A38 9 A DG 10 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? B DT 8 "O3'" ? ? ? 1_555 B A38 9 P ? ? B DT 20 B A38 21 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale one ? B A38 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B A38 21 B DG 22 1_555 ? ? ? ? ? ? ? 1.597 ? ? 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 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B A38 9 N7 ? ? A DG 4 B A38 21 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B A38 9 N6 ? ? A DG 4 B A38 21 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? 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 A38 9 N6 ? ? ? 1_555 B DG 4 O6 ? ? A A38 9 B DG 16 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog21 hydrog ? ? A A38 9 N7 ? ? ? 1_555 B DG 4 N1 ? ? A A38 9 B DG 16 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 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 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.06 108.30 2.76 0.30 N 2 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 101.60 104.50 -2.90 0.40 N 3 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 103.90 110.10 -6.20 1.00 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 110.60 108.30 2.30 0.30 N 5 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 121.49 125.10 -3.61 0.60 N 6 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 115.06 111.50 3.56 0.50 N 7 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 113.48 108.30 5.18 0.30 N 8 1 "C3'" A DC 3 ? ? "O3'" A DC 3 ? ? P A DG 4 ? ? 127.51 119.70 7.81 1.20 Y 9 1 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 101.69 110.10 -8.41 1.00 N 10 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.08 108.30 3.78 0.30 N 11 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 114.68 111.50 3.18 0.50 N 12 1 "O5'" A DA 5 ? ? "C5'" A DA 5 ? ? "C4'" A DA 5 ? ? 103.96 109.40 -5.44 0.80 N 13 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 110.20 108.30 1.90 0.30 N 14 1 C6 A DA 5 ? ? N1 A DA 5 ? ? C2 A DA 5 ? ? 122.33 118.60 3.73 0.60 N 15 1 N1 A DA 5 ? ? C2 A DA 5 ? ? N3 A DA 5 ? ? 125.51 129.30 -3.79 0.50 N 16 1 "C1'" A DA 6 ? ? "O4'" A DA 6 ? ? "C4'" A DA 6 ? ? 103.12 110.10 -6.98 1.00 N 17 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 122.33 118.60 3.73 0.60 N 18 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 125.84 129.30 -3.46 0.50 N 19 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N1 A DA 6 ? ? 114.47 117.70 -3.23 0.50 N 20 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 104.38 109.40 -5.02 0.80 N 21 1 "C1'" A DT 7 ? ? "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? 103.44 110.10 -6.66 1.00 N 22 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 113.01 108.30 4.71 0.30 N 23 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 122.34 127.20 -4.86 0.60 N 24 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 118.83 115.20 3.63 0.60 N 25 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.87 108.30 2.57 0.30 N 26 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 123.26 127.20 -3.94 0.60 N 27 1 N3 A DT 8 ? ? C4 A DT 8 ? ? O4 A DT 8 ? ? 116.20 119.90 -3.70 0.60 N 28 1 "O4'" A DG 10 ? ? "C4'" A DG 10 ? ? "C3'" A DG 10 ? ? 100.91 104.50 -3.59 0.40 N 29 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 110.41 108.30 2.11 0.30 N 30 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 121.45 125.10 -3.65 0.60 N 31 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 114.67 111.50 3.17 0.50 N 32 1 "C1'" A DC 11 ? ? "O4'" A DC 11 ? ? "C4'" A DC 11 ? ? 103.22 110.10 -6.88 1.00 N 33 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 110.54 108.30 2.24 0.30 N 34 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.66 108.30 4.36 0.30 N 35 1 C6 A DG 12 ? ? N1 A DG 12 ? ? C2 A DG 12 ? ? 121.23 125.10 -3.87 0.60 N 36 1 C5 A DG 12 ? ? C6 A DG 12 ? ? N1 A DG 12 ? ? 115.45 111.50 3.95 0.50 N 37 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 114.51 108.30 6.21 0.30 N 38 1 N3 B DC 13 ? ? C4 B DC 13 ? ? N4 B DC 13 ? ? 122.22 118.00 4.22 0.70 N 39 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 112.64 108.30 4.34 0.30 N 40 1 "O4'" B DC 15 ? ? "C4'" B DC 15 ? ? "C3'" B DC 15 ? ? 101.82 104.50 -2.68 0.40 N 41 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 112.86 108.30 4.56 0.30 N 42 1 "O4'" B DG 16 ? ? "C1'" B DG 16 ? ? N9 B DG 16 ? ? 114.43 108.30 6.13 0.30 N 43 1 C5 B DG 16 ? ? C6 B DG 16 ? ? N1 B DG 16 ? ? 114.61 111.50 3.11 0.50 N 44 1 C6 B DA 17 ? ? N1 B DA 17 ? ? C2 B DA 17 ? ? 122.28 118.60 3.68 0.60 N 45 1 N1 B DA 17 ? ? C2 B DA 17 ? ? N3 B DA 17 ? ? 125.93 129.30 -3.37 0.50 N 46 1 C5 B DA 17 ? ? C6 B DA 17 ? ? N1 B DA 17 ? ? 114.57 117.70 -3.13 0.50 N 47 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 111.10 108.30 2.80 0.30 N 48 1 N1 B DA 18 ? ? C2 B DA 18 ? ? N3 B DA 18 ? ? 126.11 129.30 -3.19 0.50 N 49 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 110.61 108.30 2.31 0.30 N 50 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 123.05 127.20 -4.15 0.60 N 51 1 N3 B DT 19 ? ? C4 B DT 19 ? ? C5 B DT 19 ? ? 119.05 115.20 3.85 0.60 N 52 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 113.07 108.30 4.77 0.30 N 53 1 C2 B DT 20 ? ? N3 B DT 20 ? ? C4 B DT 20 ? ? 122.87 127.20 -4.33 0.60 N 54 1 "C3'" B A38 21 ? ? "O3'" B A38 21 ? ? P B DG 22 ? ? 131.19 119.70 11.49 1.20 Y 55 1 "C3'" B DG 22 ? ? "C2'" B DG 22 ? ? "C1'" B DG 22 ? ? 97.30 102.40 -5.10 0.80 N 56 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 116.63 108.30 8.33 0.30 N 57 1 C6 B DG 22 ? ? N1 B DG 22 ? ? C2 B DG 22 ? ? 121.37 125.10 -3.73 0.60 N 58 1 C5 B DG 22 ? ? C6 B DG 22 ? ? N1 B DG 22 ? ? 115.09 111.50 3.59 0.50 N 59 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 115.37 108.30 7.07 0.30 N 60 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 111.75 108.30 3.45 0.30 N 61 1 C6 B DG 24 ? ? N1 B DG 24 ? ? C2 B DG 24 ? ? 121.29 125.10 -3.81 0.60 N 62 1 C5 B DG 24 ? ? C6 B DG 24 ? ? N1 B DG 24 ? ? 115.17 111.50 3.67 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 A38 9 A A38 9 ? DA ;8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE ; 2 B A38 9 B A38 21 ? DA ;8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE ; # 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 A38 O3P O N N 1 A38 P P N N 2 A38 O1P O N N 3 A38 O2P O N N 4 A38 "O5'" O N N 5 A38 "C5'" C N N 6 A38 "C4'" C N R 7 A38 "O4'" O N N 8 A38 "C3'" C N S 9 A38 "O3'" O N N 10 A38 "C2'" C N N 11 A38 "C1'" C N R 12 A38 N9 N N N 13 A38 C8 C N N 14 A38 N7 N N N 15 A38 C5 C Y N 16 A38 C6 C Y N 17 A38 N6 N N N 18 A38 N1 N Y N 19 A38 C2 C Y N 20 A38 N3 N Y N 21 A38 C4 C Y N 22 A38 O O N N 23 A38 H3P H N N 24 A38 H2P H N N 25 A38 "H5'1" H N N 26 A38 "H5'2" H N N 27 A38 "H4'" H N N 28 A38 "H3'" H N N 29 A38 HA H N N 30 A38 "H2'1" H N N 31 A38 "H2'2" H N N 32 A38 "H1'" H N N 33 A38 H7 H N N 34 A38 H6N1 H N N 35 A38 H6N2 H N N 36 A38 H2 H N N 37 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 DC OP3 O N N 74 DC P P N N 75 DC OP1 O N N 76 DC OP2 O N N 77 DC "O5'" O N N 78 DC "C5'" C N N 79 DC "C4'" C N R 80 DC "O4'" O N N 81 DC "C3'" C N S 82 DC "O3'" O N N 83 DC "C2'" C N N 84 DC "C1'" C N R 85 DC N1 N N N 86 DC C2 C N N 87 DC O2 O N N 88 DC N3 N N N 89 DC C4 C N N 90 DC N4 N N N 91 DC C5 C N N 92 DC C6 C N N 93 DC HOP3 H N N 94 DC HOP2 H N N 95 DC "H5'" H N N 96 DC "H5''" H N N 97 DC "H4'" H N N 98 DC "H3'" H N N 99 DC "HO3'" H N N 100 DC "H2'" H N N 101 DC "H2''" H N N 102 DC "H1'" H N N 103 DC H41 H N N 104 DC H42 H N N 105 DC H5 H N N 106 DC H6 H N N 107 DG OP3 O N N 108 DG P P N N 109 DG OP1 O N N 110 DG OP2 O N N 111 DG "O5'" O N N 112 DG "C5'" C N N 113 DG "C4'" C N R 114 DG "O4'" O N N 115 DG "C3'" C N S 116 DG "O3'" O N N 117 DG "C2'" C N N 118 DG "C1'" C N R 119 DG N9 N Y N 120 DG C8 C Y N 121 DG N7 N Y N 122 DG C5 C Y N 123 DG C6 C N N 124 DG O6 O N N 125 DG N1 N N N 126 DG C2 C N N 127 DG N2 N N N 128 DG N3 N N N 129 DG C4 C Y N 130 DG HOP3 H N N 131 DG HOP2 H N N 132 DG "H5'" H N N 133 DG "H5''" H N N 134 DG "H4'" H N N 135 DG "H3'" H N N 136 DG "HO3'" H N N 137 DG "H2'" H N N 138 DG "H2''" H N N 139 DG "H1'" H N N 140 DG H8 H N N 141 DG H1 H N N 142 DG H21 H N N 143 DG H22 H N N 144 DT OP3 O N N 145 DT P P N N 146 DT OP1 O N N 147 DT OP2 O N N 148 DT "O5'" O N N 149 DT "C5'" C N N 150 DT "C4'" C N R 151 DT "O4'" O N N 152 DT "C3'" C N S 153 DT "O3'" O N N 154 DT "C2'" C N N 155 DT "C1'" C N R 156 DT N1 N N N 157 DT C2 C N N 158 DT O2 O N N 159 DT N3 N N N 160 DT C4 C N N 161 DT O4 O N N 162 DT C5 C N N 163 DT C7 C N N 164 DT C6 C N N 165 DT HOP3 H N N 166 DT HOP2 H N N 167 DT "H5'" H N N 168 DT "H5''" H N N 169 DT "H4'" H N N 170 DT "H3'" H N N 171 DT "HO3'" H N N 172 DT "H2'" H N N 173 DT "H2''" H N N 174 DT "H1'" H N N 175 DT H3 H N N 176 DT H71 H N N 177 DT H72 H N N 178 DT H73 H N N 179 DT H6 H N N 180 HOH O O N N 181 HOH H1 H N N 182 HOH H2 H N N 183 # 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 A38 O3P P sing N N 1 A38 O3P H3P sing N N 2 A38 P O1P doub N N 3 A38 P O2P sing N N 4 A38 P "O5'" sing N N 5 A38 O2P H2P sing N N 6 A38 "O5'" "C5'" sing N N 7 A38 "C5'" "C4'" sing N N 8 A38 "C5'" "H5'1" sing N N 9 A38 "C5'" "H5'2" sing N N 10 A38 "C4'" "O4'" sing N N 11 A38 "C4'" "C3'" sing N N 12 A38 "C4'" "H4'" sing N N 13 A38 "O4'" "C1'" sing N N 14 A38 "C3'" "O3'" sing N N 15 A38 "C3'" "C2'" sing N N 16 A38 "C3'" "H3'" sing N N 17 A38 "O3'" HA sing N N 18 A38 "C2'" "C1'" sing N N 19 A38 "C2'" "H2'1" sing N N 20 A38 "C2'" "H2'2" sing N N 21 A38 "C1'" N9 sing N N 22 A38 "C1'" "H1'" sing N N 23 A38 N9 C8 sing N N 24 A38 N9 C4 sing N N 25 A38 C8 N7 sing N N 26 A38 C8 O doub N N 27 A38 N7 C5 sing N N 28 A38 N7 H7 sing N N 29 A38 C5 C6 doub Y N 30 A38 C5 C4 sing Y N 31 A38 C6 N6 sing N N 32 A38 C6 N1 sing Y N 33 A38 N6 H6N1 sing N N 34 A38 N6 H6N2 sing N N 35 A38 N1 C2 doub Y N 36 A38 C2 N3 sing Y N 37 A38 C2 H2 sing N N 38 A38 N3 C4 doub Y N 39 DA OP3 P sing N N 40 DA OP3 HOP3 sing N N 41 DA P OP1 doub N N 42 DA P OP2 sing N N 43 DA P "O5'" sing N N 44 DA OP2 HOP2 sing N N 45 DA "O5'" "C5'" sing N N 46 DA "C5'" "C4'" sing N N 47 DA "C5'" "H5'" sing N N 48 DA "C5'" "H5''" sing N N 49 DA "C4'" "O4'" sing N N 50 DA "C4'" "C3'" sing N N 51 DA "C4'" "H4'" sing N N 52 DA "O4'" "C1'" sing N N 53 DA "C3'" "O3'" sing N N 54 DA "C3'" "C2'" sing N N 55 DA "C3'" "H3'" sing N N 56 DA "O3'" "HO3'" sing N N 57 DA "C2'" "C1'" sing N N 58 DA "C2'" "H2'" sing N N 59 DA "C2'" "H2''" sing N N 60 DA "C1'" N9 sing N N 61 DA "C1'" "H1'" sing N N 62 DA N9 C8 sing Y N 63 DA N9 C4 sing Y N 64 DA C8 N7 doub Y N 65 DA C8 H8 sing N N 66 DA N7 C5 sing Y N 67 DA C5 C6 sing Y N 68 DA C5 C4 doub Y N 69 DA C6 N6 sing N N 70 DA C6 N1 doub Y N 71 DA N6 H61 sing N N 72 DA N6 H62 sing N N 73 DA N1 C2 sing Y N 74 DA C2 N3 doub Y N 75 DA C2 H2 sing N N 76 DA N3 C4 sing Y N 77 DC OP3 P sing N N 78 DC OP3 HOP3 sing N N 79 DC P OP1 doub N N 80 DC P OP2 sing N N 81 DC P "O5'" sing N N 82 DC OP2 HOP2 sing N N 83 DC "O5'" "C5'" sing N N 84 DC "C5'" "C4'" sing N N 85 DC "C5'" "H5'" sing N N 86 DC "C5'" "H5''" sing N N 87 DC "C4'" "O4'" sing N N 88 DC "C4'" "C3'" sing N N 89 DC "C4'" "H4'" sing N N 90 DC "O4'" "C1'" sing N N 91 DC "C3'" "O3'" sing N N 92 DC "C3'" "C2'" sing N N 93 DC "C3'" "H3'" sing N N 94 DC "O3'" "HO3'" sing N N 95 DC "C2'" "C1'" sing N N 96 DC "C2'" "H2'" sing N N 97 DC "C2'" "H2''" sing N N 98 DC "C1'" N1 sing N N 99 DC "C1'" "H1'" sing N N 100 DC N1 C2 sing N N 101 DC N1 C6 sing N N 102 DC C2 O2 doub N N 103 DC C2 N3 sing N N 104 DC N3 C4 doub N N 105 DC C4 N4 sing N N 106 DC C4 C5 sing N N 107 DC N4 H41 sing N N 108 DC N4 H42 sing N N 109 DC C5 C6 doub N N 110 DC C5 H5 sing N N 111 DC C6 H6 sing N N 112 DG OP3 P sing N N 113 DG OP3 HOP3 sing N N 114 DG P OP1 doub N N 115 DG P OP2 sing N N 116 DG P "O5'" sing N N 117 DG OP2 HOP2 sing N N 118 DG "O5'" "C5'" sing N N 119 DG "C5'" "C4'" sing N N 120 DG "C5'" "H5'" sing N N 121 DG "C5'" "H5''" sing N N 122 DG "C4'" "O4'" sing N N 123 DG "C4'" "C3'" sing N N 124 DG "C4'" "H4'" sing N N 125 DG "O4'" "C1'" sing N N 126 DG "C3'" "O3'" sing N N 127 DG "C3'" "C2'" sing N N 128 DG "C3'" "H3'" sing N N 129 DG "O3'" "HO3'" sing N N 130 DG "C2'" "C1'" sing N N 131 DG "C2'" "H2'" sing N N 132 DG "C2'" "H2''" sing N N 133 DG "C1'" N9 sing N N 134 DG "C1'" "H1'" sing N N 135 DG N9 C8 sing Y N 136 DG N9 C4 sing Y N 137 DG C8 N7 doub Y N 138 DG C8 H8 sing N N 139 DG N7 C5 sing Y N 140 DG C5 C6 sing N N 141 DG C5 C4 doub Y N 142 DG C6 O6 doub N N 143 DG C6 N1 sing N N 144 DG N1 C2 sing N N 145 DG N1 H1 sing N N 146 DG C2 N2 sing N N 147 DG C2 N3 doub N N 148 DG N2 H21 sing N N 149 DG N2 H22 sing N N 150 DG N3 C4 sing N N 151 DT OP3 P sing N N 152 DT OP3 HOP3 sing N N 153 DT P OP1 doub N N 154 DT P OP2 sing N N 155 DT P "O5'" sing N N 156 DT OP2 HOP2 sing N N 157 DT "O5'" "C5'" sing N N 158 DT "C5'" "C4'" sing N N 159 DT "C5'" "H5'" sing N N 160 DT "C5'" "H5''" sing N N 161 DT "C4'" "O4'" sing N N 162 DT "C4'" "C3'" sing N N 163 DT "C4'" "H4'" sing N N 164 DT "O4'" "C1'" sing N N 165 DT "C3'" "O3'" sing N N 166 DT "C3'" "C2'" sing N N 167 DT "C3'" "H3'" sing N N 168 DT "O3'" "HO3'" sing N N 169 DT "C2'" "C1'" sing N N 170 DT "C2'" "H2'" sing N N 171 DT "C2'" "H2''" sing N N 172 DT "C1'" N1 sing N N 173 DT "C1'" "H1'" sing N N 174 DT N1 C2 sing N N 175 DT N1 C6 sing N N 176 DT C2 O2 doub N N 177 DT C2 N3 sing N N 178 DT N3 C4 sing N N 179 DT N3 H3 sing N N 180 DT C4 O4 doub N N 181 DT C4 C5 sing N N 182 DT C5 C7 sing N N 183 DT C5 C6 doub N N 184 DT C7 H71 sing N N 185 DT C7 H72 sing N N 186 DT C7 H73 sing N N 187 DT C6 H6 sing N N 188 HOH O H1 sing N N 189 HOH O H2 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D75 'double helix' 1D75 'b-form double helix' 1D75 '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 0.121 -0.407 0.578 1.747 -12.489 -3.658 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.281 -0.481 0.828 5.502 -11.660 -1.270 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.243 -0.356 0.499 -12.730 -8.864 -7.534 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B A38 9 1_555 -2.176 5.126 0.117 -9.203 -9.088 -101.283 4 A_DG4:A3821_B A 4 ? B 21 ? 9 ? 1 A DA 5 1_555 B DT 8 1_555 -0.266 -0.498 0.159 5.333 -20.897 -0.842 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.399 -0.641 0.195 -1.554 -31.622 -1.882 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.007 -0.405 0.024 -5.433 -18.067 -0.597 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.146 -0.577 0.398 -9.594 -23.171 0.652 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A A38 9 1_555 B DG 4 1_555 1.720 -5.619 -0.262 7.002 10.150 88.631 9 A_A389:DG16_B A 9 ? B 16 ? 9 ? 1 A DG 10 1_555 B DC 3 1_555 0.410 -0.387 0.118 13.804 -6.588 -2.851 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.405 -0.799 0.966 -0.030 -22.516 -11.546 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.683 -0.591 0.386 2.816 -1.218 -3.450 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 -0.056 -0.511 3.055 -3.162 6.287 40.435 -1.362 -0.239 2.943 9.013 4.533 41.017 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 -0.081 -0.200 4.007 3.565 -13.640 34.023 1.992 0.731 3.783 -22.167 -5.794 36.749 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 DG 4 1_555 B A38 9 1_555 1.370 -1.445 2.751 6.698 6.123 65.062 -1.545 -1.034 2.734 5.664 -6.196 65.622 3 AA_DC3DG4:A3821DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B A38 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.309 2.324 3.414 -2.228 5.173 4.948 -5.618 -7.712 3.949 44.758 19.279 7.496 4 AA_DG4DA5:DT20A3821_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 0.236 -0.440 3.382 -2.872 3.961 32.747 -1.456 -0.911 3.275 6.977 5.059 33.100 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 0.014 -0.497 3.420 -1.366 -8.536 32.175 0.650 -0.268 3.432 -15.065 2.412 33.286 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 -0.198 -0.035 3.411 1.234 1.192 42.857 -0.171 0.399 3.402 1.630 -1.688 42.889 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 A38 9 1_555 B DG 4 1_555 0.163 -3.200 2.550 -176.344 -5.378 3.048 -1.563 -1.324 0.002 -2.742 89.911 176.428 8 AA_DT8A389:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A A38 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 -1.012 -2.901 -2.600 151.790 -91.502 89.583 -1.879 -0.204 -1.384 -45.962 -76.244 178.039 9 AA_A389DG10:DC15DG16_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 -0.164 0.827 3.762 -6.554 -13.356 36.043 3.053 -0.643 3.248 -20.542 10.080 38.898 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 -0.151 0.150 3.523 5.135 1.385 36.779 0.037 0.973 3.475 2.181 -8.087 37.148 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 1D75 _atom_sites.fract_transf_matrix[1][1] 0.039246 _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] 0.023901 _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] 0.015406 _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_