data_1S1K # _entry.id 1S1K # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1S1K pdb_00001s1k 10.2210/pdb1s1k/pdb NDB BD0068 ? ? RCSB RCSB021250 ? ? WWPDB D_1000021250 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1P4Z _pdbx_database_related.details 'Unmodified ACT strand' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S1K _pdbx_database_status.recvd_initial_deposition_date 2004-01-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Hays, F.A.' 1 'Watson, J.' 2 'Ho, P.S.' 3 # _citation.id primary _citation.title 'Influence of minor groove substituents on the structure of DNA holliday junctions.' _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 9813 _citation.page_last 9822 _citation.year 2004 _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 15274635 _citation.pdbx_database_id_DOI 10.1021/bi049461d # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Jones, Z.J.' 2 ? primary 'Ho, P.S.' 3 ? # _cell.entry_id 1S1K _cell.length_a 32.957 _cell.length_b 32.957 _cell.length_c 88.556 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S1K _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # 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 "5'-D(*CP*CP*(1AP)P*GP*TP*AP*CP*TP*GP*G)-3'" 3060.019 1 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 40 ? ? ? ? # _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)(DC)(1AP)(DG)(DT)(DA)(DC)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAGTACTGG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 DC n 1 3 1AP n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 DT n 1 9 DG n 1 10 DG n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1S1K _struct_ref.pdbx_db_accession 1S1K _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1S1K _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1S1K _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # 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 1AP 'DNA linking' n '2,6-DIAMINOPURINE NUCLEOTIDE' ? 'C10 H15 N6 O6 P' 346.236 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # _exptl.entry_id 1S1K _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 38.5 _exptl_crystal.description ? _exptl_crystal.density_Matthews 2.02 _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 ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.50 _exptl_crystal_grow.pdbx_details '5mM TRIS(HCl), 23mM CaAcetate, 16% MPD, .6mM DNA against 28% MPD at RT, pH 7.50, VAPOR DIFFUSION, SITTING DROP' _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 'TRIS(HCl)' ? ? ? 1 2 1 CaAcetate ? ? ? 1 3 1 '16% MPD' ? ? ? 1 4 1 DNA ? ? ? 1 5 ? water ? ? ? 1 6 ? '28% MPD' ? ? ? 1 7 ? 'TRIS(HCl)' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2002-01-08 _diffrn_detector.details 'BENT CONICAL SI-MIRROR (RH COATING)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'BENT GE(111) MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-BM-C' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-BM-C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9 # _reflns.entry_id 1S1K _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 17.50 _reflns.d_resolution_high 1.850 _reflns.number_obs 2528 _reflns.number_all 2528 _reflns.percent_possible_obs 96.3 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 8.80 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.85 _reflns_shell.d_res_low 1.92 _reflns_shell.percent_possible_all 72.2 _reflns_shell.Rmerge_I_obs 0.245 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.980 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1S1K _refine.ls_number_reflns_obs 2413 _refine.ls_number_reflns_all 2528 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 29235.77 _refine.pdbx_data_cutoff_low_absF 0.0 _refine.pdbx_data_cutoff_high_rms_absF 29235.77 _refine.ls_d_res_low 17.49 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 93.9 _refine.ls_R_factor_obs 0.232 _refine.ls_R_factor_all 0.253 _refine.ls_R_factor_R_work 0.232 _refine.ls_R_factor_R_free 0.258 _refine.ls_R_factor_R_free_error 0.017 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.400 _refine.ls_number_reflns_R_free 228 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 14.0 _refine.aniso_B[1][1] 3.22 _refine.aniso_B[2][2] 3.22 _refine.aniso_B[3][3] -6.45 _refine.aniso_B[1][2] 3.51 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 1P4Z _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values CNS _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1S1K _refine_analyze.Luzzati_coordinate_error_obs 0.25 _refine_analyze.Luzzati_sigma_a_obs 0.26 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.26 _refine_analyze.Luzzati_sigma_a_free 0.33 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 203 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 246 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 17.49 # 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 c_bond_d 0.067 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 6.20 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 21.60 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 5.46 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.90 _refine_ls_shell.d_res_low 2.02 _refine_ls_shell.number_reflns_R_work 287 _refine_ls_shell.R_factor_R_work 0.308 _refine_ls_shell.percent_reflns_obs 80.70 _refine_ls_shell.R_factor_R_free 0.4 _refine_ls_shell.R_factor_R_free_error 0.069 _refine_ls_shell.percent_reflns_R_free 10.60 _refine_ls_shell.number_reflns_R_free 34 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1S1K _struct.title 'INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1S1K _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, 2, 6-Diaminopurine, Minor groove interactions, 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 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 DC 2 "O3'" ? ? ? 1_555 A 1AP 3 P ? ? A DC 2 A 1AP 3 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale2 covale one ? A 1AP 3 "O3'" ? ? ? 1_555 A DG 4 P ? ? A 1AP 3 A DG 4 1_555 ? ? ? ? ? ? ? 1.634 ? ? covale3 covale none ? A 1AP 3 "O3'" ? ? ? 1_555 A DG 4 OP1 ? ? A 1AP 3 A DG 4 1_555 ? ? ? ? ? ? ? 1.935 ? ? metalc1 metalc ? ? A DT 5 OP1 ? ? ? 1_555 D NA . NA ? ? A DT 5 A NA 15 1_555 ? ? ? ? ? ? ? 2.502 ? ? metalc2 metalc ? ? A DC 7 OP2 ? ? ? 1_555 C CA . CA ? ? A DC 7 A CA 14 1_555 ? ? ? ? ? ? ? 2.539 ? ? metalc3 metalc ? ? A DC 7 OP2 ? ? ? 8_555 C CA . CA ? ? A DC 7 A CA 14 1_555 ? ? ? ? ? ? ? 2.448 ? ? metalc4 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 11 A HOH 20 1_555 ? ? ? ? ? ? ? 3.150 ? ? metalc5 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 11 A HOH 20 8_555 ? ? ? ? ? ? ? 3.173 ? ? metalc6 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 11 A HOH 45 1_555 ? ? ? ? ? ? ? 2.830 ? ? metalc7 metalc ? ? B CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 11 A HOH 45 8_555 ? ? ? ? ? ? ? 2.840 ? ? metalc8 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 14 A HOH 23 8_555 ? ? ? ? ? ? ? 3.355 ? ? metalc9 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 14 A HOH 28 1_555 ? ? ? ? ? ? ? 2.375 ? ? metalc10 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 14 A HOH 28 8_555 ? ? ? ? ? ? ? 2.342 ? ? metalc11 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 15 A HOH 31 1_555 ? ? ? ? ? ? ? 1.795 ? ? metalc12 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 15 A HOH 36 1_555 ? ? ? ? ? ? ? 2.731 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 1AP 3 N2 ? ? ? 1_555 A DT 8 O2 ? ? A 1AP 3 A DT 8 12_545 ? ? ? ? ? ? '1AP-DT MISPAIR' ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 A DA 6 N1 ? ? A DT 5 A DA 6 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 A DA 6 N6 ? ? A DT 5 A DA 6 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 A DT 5 N3 ? ? A DA 6 A DT 5 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DT 5 O4 ? ? A DA 6 A DT 5 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 O2 ? ? ? 1_555 A 1AP 3 N2 ? ? A DT 8 A 1AP 3 12_545 ? ? ? ? ? ? 'DT-1AP MISPAIR' ? ? ? hydrog19 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 12_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A CA 11 ? 2 'BINDING SITE FOR RESIDUE CA A 11' AC2 Software A CA 14 ? 4 'BINDING SITE FOR RESIDUE CA A 14' AC3 Software A NA 15 ? 3 'BINDING SITE FOR RESIDUE NA A 15' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 HOH E . ? HOH A 45 . ? 1_555 ? 2 AC1 2 HOH E . ? HOH A 45 . ? 8_555 ? 3 AC2 4 DC A 7 ? DC A 7 . ? 1_555 ? 4 AC2 4 DC A 7 ? DC A 7 . ? 8_555 ? 5 AC2 4 HOH E . ? HOH A 28 . ? 1_555 ? 6 AC2 4 HOH E . ? HOH A 28 . ? 8_555 ? 7 AC3 3 DT A 5 ? DT A 5 . ? 1_555 ? 8 AC3 3 HOH E . ? HOH A 31 . ? 1_555 ? 9 AC3 3 HOH E . ? HOH A 36 . ? 1_555 ? # _database_PDB_matrix.entry_id 1S1K _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 # _atom_sites.entry_id 1S1K _atom_sites.fract_transf_matrix[1][1] 0.030343 _atom_sites.fract_transf_matrix[1][2] 0.017518 _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] 0.035037 _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] 0.011292 _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 CA N NA O P # 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 DC 2 2 2 DC C A . n A 1 3 1AP 3 3 3 1AP DAP A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . 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 B 2 CA 1 11 11 CA CA A . C 2 CA 1 14 14 CA CA A . D 3 NA 1 15 15 NA NA A . E 4 HOH 1 12 12 HOH WAT A . E 4 HOH 2 13 13 HOH WAT A . E 4 HOH 3 16 16 HOH WAT A . E 4 HOH 4 17 17 HOH WAT A . E 4 HOH 5 18 18 HOH WAT A . E 4 HOH 6 19 19 HOH WAT A . E 4 HOH 7 20 20 HOH WAT A . E 4 HOH 8 21 21 HOH WAT A . E 4 HOH 9 22 22 HOH WAT A . E 4 HOH 10 23 23 HOH WAT A . E 4 HOH 11 24 24 HOH WAT A . E 4 HOH 12 25 25 HOH WAT A . E 4 HOH 13 26 26 HOH WAT A . E 4 HOH 14 27 27 HOH WAT A . E 4 HOH 15 28 28 HOH WAT A . E 4 HOH 16 29 29 HOH WAT A . E 4 HOH 17 30 30 HOH WAT A . E 4 HOH 18 31 31 HOH WAT A . E 4 HOH 19 32 32 HOH WAT A . E 4 HOH 20 33 33 HOH WAT A . E 4 HOH 21 34 34 HOH WAT A . E 4 HOH 22 35 35 HOH WAT A . E 4 HOH 23 36 36 HOH WAT A . E 4 HOH 24 37 37 HOH WAT A . E 4 HOH 25 38 38 HOH WAT A . E 4 HOH 26 41 41 HOH WAT A . E 4 HOH 27 42 42 HOH WAT A . E 4 HOH 28 43 43 HOH WAT A . E 4 HOH 29 44 44 HOH WAT A . E 4 HOH 30 45 45 HOH WAT A . E 4 HOH 31 46 46 HOH WAT A . E 4 HOH 32 47 47 HOH WAT A . E 4 HOH 33 48 48 HOH WAT A . E 4 HOH 34 49 49 HOH WAT A . E 4 HOH 35 50 50 HOH WAT A . E 4 HOH 36 51 51 HOH WAT A . E 4 HOH 37 52 52 HOH WAT A . E 4 HOH 38 53 53 HOH WAT A . E 4 HOH 39 54 54 HOH WAT A . E 4 HOH 40 55 55 HOH WAT A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 1AP _pdbx_struct_mod_residue.label_seq_id 3 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 1AP _pdbx_struct_mod_residue.auth_seq_id 3 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DA _pdbx_struct_mod_residue.details '2,6-DIAMINOPURINE NUCLEOTIDE' # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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.vector[1] _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.vector[2] _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[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 12_545 x,x-y-1,-z+1/6 0.5000000000 0.8660254038 0.0000000000 16.4785000000 0.8660254038 -0.5000000000 0.0000000000 -28.5415992325 0.0000000000 0.0000000000 -1.0000000000 14.7593333333 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CA 11 ? B CA . 2 1 A CA 14 ? C CA . 3 1 A HOH 32 ? E HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? A DT 5 ? A DT 5 ? 1_555 NA ? D NA . ? A NA 15 ? 1_555 O ? E HOH . ? A HOH 31 ? 1_555 101.0 ? 2 OP1 ? A DT 5 ? A DT 5 ? 1_555 NA ? D NA . ? A NA 15 ? 1_555 O ? E HOH . ? A HOH 36 ? 1_555 57.7 ? 3 O ? E HOH . ? A HOH 31 ? 1_555 NA ? D NA . ? A NA 15 ? 1_555 O ? E HOH . ? A HOH 36 ? 1_555 145.2 ? 4 OP2 ? A DC 7 ? A DC 7 ? 1_555 CA ? C CA . ? A CA 14 ? 1_555 OP2 ? A DC 7 ? A DC 7 ? 8_555 169.6 ? 5 OP2 ? A DC 7 ? A DC 7 ? 1_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 23 ? 8_555 105.6 ? 6 OP2 ? A DC 7 ? A DC 7 ? 8_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 23 ? 8_555 72.0 ? 7 OP2 ? A DC 7 ? A DC 7 ? 1_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 81.5 ? 8 OP2 ? A DC 7 ? A DC 7 ? 8_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 104.3 ? 9 O ? E HOH . ? A HOH 23 ? 8_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 159.0 ? 10 OP2 ? A DC 7 ? A DC 7 ? 1_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 8_555 102.5 ? 11 OP2 ? A DC 7 ? A DC 7 ? 8_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 8_555 84.2 ? 12 O ? E HOH . ? A HOH 23 ? 8_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 8_555 52.3 ? 13 O ? E HOH . ? A HOH 28 ? 1_555 CA ? C CA . ? A CA 14 ? 1_555 O ? E HOH . ? A HOH 28 ? 8_555 107.2 ? 14 O ? E HOH . ? A HOH 20 ? 1_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 20 ? 8_555 107.8 ? 15 O ? E HOH . ? A HOH 20 ? 1_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 45 ? 1_555 125.9 ? 16 O ? E HOH . ? A HOH 20 ? 8_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 45 ? 1_555 107.2 ? 17 O ? E HOH . ? A HOH 20 ? 1_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 45 ? 8_555 107.6 ? 18 O ? E HOH . ? A HOH 20 ? 8_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 45 ? 8_555 124.7 ? 19 O ? E HOH . ? A HOH 45 ? 1_555 CA ? B CA . ? A CA 11 ? 1_555 O ? E HOH . ? A HOH 45 ? 8_555 83.8 ? # 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 2004-08-31 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2023-08-23 # _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' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' # 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' atom_site 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_initial_refinement_model 6 4 'Structure model' pdbx_struct_conn_angle 7 4 'Structure model' struct_conn 8 4 'Structure model' struct_site # 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' '_atom_site.occupancy' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 23 4 'Structure model' '_pdbx_struct_conn_angle.value' 24 4 'Structure model' '_struct_conn.pdbx_dist_value' 25 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 26 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr1_symmetry' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 4 'Structure model' '_struct_conn.ptnr2_symmetry' 40 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 41 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 42 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 EPMR phasing . ? 3 CNS refinement 1.0 ? 4 # _pdbx_database_remark.id 300 _pdbx_database_remark.text ;BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE FULL BIOLOGICAL UNIT CONSISTS OF TWO STRANDS FORMING A B-DNA DUPLEX STRUCTURE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ; # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "O4'" A DC 2 ? ? O A HOH 48 ? ? 2.03 2 1 OP2 A DA 6 ? ? O A HOH 37 ? ? 2.04 3 1 O2 A DT 5 ? ? O A HOH 49 ? ? 2.10 4 1 OP1 A DG 9 ? ? O A HOH 16 ? ? 2.11 5 1 O A HOH 35 ? ? O A HOH 41 ? ? 2.11 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 37 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 37 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 8_555 _pdbx_validate_symm_contact.dist 1.34 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 1.463 1.516 -0.053 0.008 N 2 1 "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 1.606 1.519 0.087 0.010 N 3 1 C4 A DC 1 ? ? C5 A DC 1 ? ? 1.478 1.425 0.053 0.008 N 4 1 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.464 1.339 0.125 0.008 N 5 1 P A DC 2 ? ? OP2 A DC 2 ? ? 1.600 1.485 0.115 0.017 N 6 1 "C3'" A DC 2 ? ? "C2'" A DC 2 ? ? 1.468 1.516 -0.048 0.008 N 7 1 C4 A DC 2 ? ? N4 A DC 2 ? ? 1.441 1.335 0.106 0.009 N 8 1 N1 A DC 2 ? ? C2 A DC 2 ? ? 1.480 1.397 0.083 0.010 N 9 1 C5 A DC 2 ? ? C6 A DC 2 ? ? 1.288 1.339 -0.051 0.008 N 10 1 P A DG 4 ? ? "O5'" A DG 4 ? ? 1.663 1.593 0.070 0.010 N 11 1 "O3'" A DG 4 ? ? "C3'" A DG 4 ? ? 1.298 1.419 -0.121 0.006 N 12 1 C2 A DG 4 ? ? N3 A DG 4 ? ? 1.382 1.323 0.059 0.008 N 13 1 C4 A DG 4 ? ? C5 A DG 4 ? ? 1.296 1.379 -0.083 0.007 N 14 1 C8 A DG 4 ? ? N9 A DG 4 ? ? 1.279 1.374 -0.095 0.007 N 15 1 "O3'" A DG 4 ? ? P A DT 5 ? ? 1.526 1.607 -0.081 0.012 Y 16 1 "C2'" A DT 5 ? ? "C1'" A DT 5 ? ? 1.634 1.519 0.115 0.010 N 17 1 "O3'" A DT 5 ? ? "C3'" A DT 5 ? ? 1.255 1.419 -0.164 0.006 N 18 1 "C1'" A DT 5 ? ? N1 A DT 5 ? ? 1.594 1.488 0.106 0.013 N 19 1 C2 A DT 5 ? ? N3 A DT 5 ? ? 1.296 1.373 -0.077 0.008 N 20 1 C4 A DT 5 ? ? C5 A DT 5 ? ? 1.343 1.445 -0.102 0.009 N 21 1 C6 A DT 5 ? ? N1 A DT 5 ? ? 1.429 1.378 0.051 0.007 N 22 1 C2 A DT 5 ? ? O2 A DT 5 ? ? 1.310 1.220 0.090 0.008 N 23 1 C4 A DT 5 ? ? O4 A DT 5 ? ? 1.154 1.228 -0.074 0.009 N 24 1 C5 A DT 5 ? ? C7 A DT 5 ? ? 1.453 1.496 -0.043 0.006 N 25 1 P A DA 6 ? ? OP1 A DA 6 ? ? 1.286 1.485 -0.199 0.017 N 26 1 P A DA 6 ? ? OP2 A DA 6 ? ? 1.620 1.485 0.135 0.017 N 27 1 P A DA 6 ? ? "O5'" A DA 6 ? ? 1.532 1.593 -0.061 0.010 N 28 1 C2 A DA 6 ? ? N3 A DA 6 ? ? 1.251 1.331 -0.080 0.009 N 29 1 N3 A DA 6 ? ? C4 A DA 6 ? ? 1.306 1.344 -0.038 0.006 N 30 1 C5 A DA 6 ? ? C6 A DA 6 ? ? 1.530 1.406 0.124 0.009 N 31 1 C6 A DA 6 ? ? N6 A DA 6 ? ? 1.173 1.335 -0.162 0.008 N 32 1 P A DC 7 ? ? "O5'" A DC 7 ? ? 1.484 1.593 -0.109 0.010 N 33 1 C2 A DC 7 ? ? O2 A DC 7 ? ? 1.180 1.240 -0.060 0.009 N 34 1 C4 A DC 7 ? ? N4 A DC 7 ? ? 1.247 1.335 -0.088 0.009 N 35 1 N1 A DC 7 ? ? C6 A DC 7 ? ? 1.294 1.367 -0.073 0.006 N 36 1 "O3'" A DC 7 ? ? P A DT 8 ? ? 1.739 1.607 0.132 0.012 Y 37 1 P A DT 8 ? ? OP2 A DT 8 ? ? 1.661 1.485 0.176 0.017 N 38 1 "C2'" A DT 8 ? ? "C1'" A DT 8 ? ? 1.408 1.518 -0.110 0.010 N 39 1 "O4'" A DT 8 ? ? "C4'" A DT 8 ? ? 1.331 1.446 -0.115 0.010 N 40 1 "O3'" A DT 8 ? ? "C3'" A DT 8 ? ? 1.379 1.419 -0.040 0.006 N 41 1 C5 A DT 8 ? ? C6 A DT 8 ? ? 1.260 1.339 -0.079 0.007 N 42 1 C2 A DT 8 ? ? O2 A DT 8 ? ? 1.101 1.220 -0.119 0.008 N 43 1 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.404 1.496 -0.092 0.006 N 44 1 P A DG 9 ? ? OP1 A DG 9 ? ? 1.357 1.485 -0.128 0.017 N 45 1 P A DG 9 ? ? OP2 A DG 9 ? ? 1.342 1.485 -0.143 0.017 N 46 1 C2 A DG 9 ? ? N3 A DG 9 ? ? 1.414 1.323 0.091 0.008 N 47 1 N3 A DG 9 ? ? C4 A DG 9 ? ? 1.282 1.350 -0.068 0.007 N 48 1 C6 A DG 9 ? ? N1 A DG 9 ? ? 1.335 1.391 -0.056 0.007 N 49 1 C2 A DG 9 ? ? N2 A DG 9 ? ? 1.490 1.341 0.149 0.010 N 50 1 C6 A DG 9 ? ? O6 A DG 9 ? ? 1.146 1.237 -0.091 0.009 N 51 1 P A DG 10 ? ? "O5'" A DG 10 ? ? 1.499 1.593 -0.094 0.010 N 52 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? 1.496 1.420 0.076 0.011 N 53 1 "O3'" A DG 10 ? ? "C3'" A DG 10 ? ? 1.307 1.419 -0.112 0.006 N 54 1 N3 A DG 10 ? ? C4 A DG 10 ? ? 1.494 1.350 0.144 0.007 N 55 1 C5 A DG 10 ? ? C6 A DG 10 ? ? 1.347 1.419 -0.072 0.010 N 56 1 C6 A DG 10 ? ? N1 A DG 10 ? ? 1.331 1.391 -0.060 0.007 N 57 1 C5 A DG 10 ? ? N7 A DG 10 ? ? 1.343 1.388 -0.045 0.006 N 58 1 N9 A DG 10 ? ? C4 A DG 10 ? ? 1.424 1.375 0.049 0.008 N 59 1 C2 A DG 10 ? ? N2 A DG 10 ? ? 1.425 1.341 0.084 0.010 N # 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 ? ? 112.17 108.30 3.87 0.30 N 2 1 N1 A DC 1 ? ? C2 A DC 1 ? ? N3 A DC 1 ? ? 124.77 119.20 5.57 0.70 N 3 1 N3 A DC 1 ? ? C4 A DC 1 ? ? C5 A DC 1 ? ? 118.71 121.90 -3.19 0.40 N 4 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 114.02 118.90 -4.88 0.60 N 5 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 125.92 110.50 15.42 1.10 Y 6 1 "O5'" A DC 2 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 97.44 105.70 -8.26 0.90 N 7 1 "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 102.25 114.10 -11.85 1.80 N 8 1 "C1'" A DC 2 ? ? "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 102.11 110.10 -7.99 1.00 N 9 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 115.68 108.30 7.38 0.30 N 10 1 "O3'" A 1AP 3 ? ? P A DG 4 ? ? OP2 A DG 4 ? ? 136.89 110.50 26.39 1.10 Y 11 1 "O3'" A 1AP 3 ? ? P A DG 4 ? ? OP1 A DG 4 ? ? 76.52 105.20 -28.68 2.20 Y 12 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 109.70 106.00 3.70 0.60 N 13 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 110.41 108.30 2.11 0.30 N 14 1 N1 A DG 4 ? ? C2 A DG 4 ? ? N3 A DG 4 ? ? 119.99 123.90 -3.91 0.60 N 15 1 C2 A DG 4 ? ? N3 A DG 4 ? ? C4 A DG 4 ? ? 115.18 111.90 3.28 0.50 N 16 1 C4 A DG 4 ? ? C5 A DG 4 ? ? N7 A DG 4 ? ? 107.64 110.80 -3.16 0.40 N 17 1 C5 A DG 4 ? ? N7 A DG 4 ? ? C8 A DG 4 ? ? 107.49 104.30 3.19 0.50 N 18 1 "O3'" A DG 4 ? ? P A DT 5 ? ? OP2 A DT 5 ? ? 118.26 110.50 7.76 1.10 Y 19 1 "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? 110.85 106.00 4.85 0.60 N 20 1 "C2'" A DT 5 ? ? "C3'" A DT 5 ? ? "O3'" A DT 5 ? ? 82.57 109.40 -26.83 2.50 N 21 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.65 108.30 2.35 0.30 N 22 1 C2 A DT 5 ? ? N3 A DT 5 ? ? C4 A DT 5 ? ? 132.01 127.20 4.81 0.60 N 23 1 "O3'" A DT 5 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 90.29 105.20 -14.91 2.20 Y 24 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 98.26 105.70 -7.44 0.90 N 25 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 122.22 110.70 11.52 1.20 N 26 1 "C1'" A DA 6 ? ? "O4'" A DA 6 ? ? "C4'" A DA 6 ? ? 117.68 110.30 7.38 0.70 N 27 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 113.63 118.60 -4.97 0.60 N 28 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 133.66 129.30 4.36 0.50 N 29 1 C2 A DA 6 ? ? N3 A DA 6 ? ? C4 A DA 6 ? ? 115.49 110.60 4.89 0.50 N 30 1 N3 A DA 6 ? ? C4 A DA 6 ? ? C5 A DA 6 ? ? 122.31 126.80 -4.49 0.70 N 31 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 116.89 113.80 3.09 0.50 N 32 1 "O3'" A DA 6 ? ? P A DC 7 ? ? OP2 A DC 7 ? ? 124.09 110.50 13.59 1.10 Y 33 1 "O3'" A DA 6 ? ? P A DC 7 ? ? OP1 A DC 7 ? ? 78.29 105.20 -26.91 2.20 Y 34 1 "O5'" A DC 7 ? ? P A DC 7 ? ? OP1 A DC 7 ? ? 129.28 110.70 18.58 1.20 N 35 1 "O5'" A DC 7 ? ? P A DC 7 ? ? OP2 A DC 7 ? ? 98.33 105.70 -7.37 0.90 N 36 1 "C5'" A DC 7 ? ? "C4'" A DC 7 ? ? "O4'" A DC 7 ? ? 86.73 109.30 -22.57 1.90 N 37 1 C2 A DC 7 ? ? N3 A DC 7 ? ? C4 A DC 7 ? ? 114.26 119.90 -5.64 0.50 N 38 1 "C1'" A DT 8 ? ? "O4'" A DT 8 ? ? "C4'" A DT 8 ? ? 115.51 110.30 5.21 0.70 N 39 1 "O3'" A DT 8 ? ? P A DG 9 ? ? "O5'" A DG 9 ? ? 123.19 104.00 19.19 1.90 Y 40 1 "O3'" A DT 8 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 123.49 110.50 12.99 1.10 Y 41 1 "O3'" A DT 8 ? ? P A DG 9 ? ? OP1 A DG 9 ? ? 83.07 105.20 -22.13 2.20 Y 42 1 "O5'" A DG 9 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 97.11 105.70 -8.59 0.90 N 43 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 100.16 104.50 -4.34 0.40 N 44 1 "C5'" A DG 9 ? ? "C4'" A DG 9 ? ? "O4'" A DG 9 ? ? 96.91 109.30 -12.39 1.90 N 45 1 "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 94.24 102.40 -8.16 0.80 N 46 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? "C2'" A DG 9 ? ? 112.31 106.80 5.51 0.50 N 47 1 C6 A DG 9 ? ? C5 A DG 9 ? ? N7 A DG 9 ? ? 126.10 130.40 -4.30 0.60 N 48 1 "O3'" A DG 9 ? ? P A DG 10 ? ? "O5'" A DG 10 ? ? 117.97 104.00 13.97 1.90 Y 49 1 "O5'" A DG 10 ? ? P A DG 10 ? ? OP1 A DG 10 ? ? 91.56 105.70 -14.14 0.90 N 50 1 "C5'" A DG 10 ? ? "C4'" A DG 10 ? ? "O4'" A DG 10 ? ? 121.80 109.80 12.00 1.10 N 51 1 "C1'" A DG 10 ? ? "O4'" A DG 10 ? ? "C4'" A DG 10 ? ? 104.03 110.10 -6.07 1.00 N 52 1 "C4'" A DG 10 ? ? "C3'" A DG 10 ? ? "O3'" A DG 10 ? ? 85.38 109.70 -24.32 2.50 N 53 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 110.32 108.30 2.02 0.30 N 54 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 132.11 125.10 7.01 0.60 N 55 1 C2 A DG 10 ? ? N3 A DG 10 ? ? C4 A DG 10 ? ? 108.62 111.90 -3.28 0.50 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA A 6 ? ? 0.086 'SIDE CHAIN' 2 1 DC A 7 ? ? 0.128 'SIDE CHAIN' 3 1 DG A 9 ? ? 0.083 'SIDE CHAIN' 4 1 DG A 10 ? ? 0.120 'SIDE CHAIN' # 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 1AP N1 N Y N 1 1AP C2 C Y N 2 1AP C4 C Y N 3 1AP C5 C Y N 4 1AP C6 C Y N 5 1AP C8 C Y N 6 1AP N2 N N N 7 1AP N3 N Y N 8 1AP N9 N Y N 9 1AP N7 N Y N 10 1AP N6 N N N 11 1AP P P N N 12 1AP OP1 O N N 13 1AP OP2 O N N 14 1AP "O5'" O N N 15 1AP "C5'" C N N 16 1AP "C4'" C N R 17 1AP "O4'" O N N 18 1AP "C1'" C N R 19 1AP "C2'" C N N 20 1AP "C3'" C N S 21 1AP "O3'" O N N 22 1AP OP3 O N N 23 1AP H81 H N N 24 1AP HN21 H N N 25 1AP HN22 H N N 26 1AP HN61 H N N 27 1AP HN62 H N N 28 1AP H1P H N N 29 1AP H52 H N N 30 1AP H51 H N N 31 1AP H4 H N N 32 1AP H11 H N N 33 1AP H21 H N N 34 1AP H22 H N N 35 1AP H31 H N N 36 1AP HO31 H N N 37 1AP H3P H N N 38 CA CA CA N N 39 DA OP3 O N N 40 DA P P N N 41 DA OP1 O N N 42 DA OP2 O N N 43 DA "O5'" O N N 44 DA "C5'" C N N 45 DA "C4'" C N R 46 DA "O4'" O N N 47 DA "C3'" C N S 48 DA "O3'" O N N 49 DA "C2'" C N N 50 DA "C1'" C N R 51 DA N9 N Y N 52 DA C8 C Y N 53 DA N7 N Y N 54 DA C5 C Y N 55 DA C6 C Y N 56 DA N6 N N N 57 DA N1 N Y N 58 DA C2 C Y N 59 DA N3 N Y N 60 DA C4 C Y N 61 DA HOP3 H N N 62 DA HOP2 H N N 63 DA "H5'" H N N 64 DA "H5''" H N N 65 DA "H4'" H N N 66 DA "H3'" H N N 67 DA "HO3'" H N N 68 DA "H2'" H N N 69 DA "H2''" H N N 70 DA "H1'" H N N 71 DA H8 H N N 72 DA H61 H N N 73 DA H62 H N N 74 DA H2 H N N 75 DC OP3 O N N 76 DC P P N N 77 DC OP1 O N N 78 DC OP2 O N N 79 DC "O5'" O N N 80 DC "C5'" C N N 81 DC "C4'" C N R 82 DC "O4'" O N N 83 DC "C3'" C N S 84 DC "O3'" O N N 85 DC "C2'" C N N 86 DC "C1'" C N R 87 DC N1 N N N 88 DC C2 C N N 89 DC O2 O N N 90 DC N3 N N N 91 DC C4 C N N 92 DC N4 N N N 93 DC C5 C N N 94 DC C6 C N N 95 DC HOP3 H N N 96 DC HOP2 H N N 97 DC "H5'" H N N 98 DC "H5''" H N N 99 DC "H4'" H N N 100 DC "H3'" H N N 101 DC "HO3'" H N N 102 DC "H2'" H N N 103 DC "H2''" H N N 104 DC "H1'" H N N 105 DC H41 H N N 106 DC H42 H N N 107 DC H5 H N N 108 DC H6 H N N 109 DG OP3 O N N 110 DG P P N N 111 DG OP1 O N N 112 DG OP2 O N N 113 DG "O5'" O N N 114 DG "C5'" C N N 115 DG "C4'" C N R 116 DG "O4'" O N N 117 DG "C3'" C N S 118 DG "O3'" O N N 119 DG "C2'" C N N 120 DG "C1'" C N R 121 DG N9 N Y N 122 DG C8 C Y N 123 DG N7 N Y N 124 DG C5 C Y N 125 DG C6 C N N 126 DG O6 O N N 127 DG N1 N N N 128 DG C2 C N N 129 DG N2 N N N 130 DG N3 N N N 131 DG C4 C Y N 132 DG HOP3 H N N 133 DG HOP2 H N N 134 DG "H5'" H N N 135 DG "H5''" H N N 136 DG "H4'" H N N 137 DG "H3'" H N N 138 DG "HO3'" H N N 139 DG "H2'" H N N 140 DG "H2''" H N N 141 DG "H1'" H N N 142 DG H8 H N N 143 DG H1 H N N 144 DG H21 H N N 145 DG H22 H N N 146 DT OP3 O N N 147 DT P P N N 148 DT OP1 O N N 149 DT OP2 O N N 150 DT "O5'" O N N 151 DT "C5'" C N N 152 DT "C4'" C N R 153 DT "O4'" O N N 154 DT "C3'" C N S 155 DT "O3'" O N N 156 DT "C2'" C N N 157 DT "C1'" C N R 158 DT N1 N N N 159 DT C2 C N N 160 DT O2 O N N 161 DT N3 N N N 162 DT C4 C N N 163 DT O4 O N N 164 DT C5 C N N 165 DT C7 C N N 166 DT C6 C N N 167 DT HOP3 H N N 168 DT HOP2 H N N 169 DT "H5'" H N N 170 DT "H5''" H N N 171 DT "H4'" H N N 172 DT "H3'" H N N 173 DT "HO3'" H N N 174 DT "H2'" H N N 175 DT "H2''" H N N 176 DT "H1'" H N N 177 DT H3 H N N 178 DT H71 H N N 179 DT H72 H N N 180 DT H73 H N N 181 DT H6 H N N 182 HOH O O N N 183 HOH H1 H N N 184 HOH H2 H N N 185 NA NA NA N N 186 # 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 1AP N1 C2 sing Y N 1 1AP N1 C6 doub Y N 2 1AP C2 N2 sing N N 3 1AP C2 N3 doub Y N 4 1AP C4 C5 doub Y N 5 1AP C4 N3 sing Y N 6 1AP C4 N9 sing Y N 7 1AP C5 C6 sing Y N 8 1AP C5 N7 sing Y N 9 1AP C6 N6 sing N N 10 1AP C8 N9 sing Y N 11 1AP C8 N7 doub Y N 12 1AP C8 H81 sing N N 13 1AP N2 HN21 sing N N 14 1AP N2 HN22 sing N N 15 1AP N9 "C1'" sing N N 16 1AP N6 HN61 sing N N 17 1AP N6 HN62 sing N N 18 1AP P OP1 sing N N 19 1AP P OP2 doub N N 20 1AP P "O5'" sing N N 21 1AP P OP3 sing N N 22 1AP OP1 H1P sing N N 23 1AP "O5'" "C5'" sing N N 24 1AP "C5'" "C4'" sing N N 25 1AP "C5'" H52 sing N N 26 1AP "C5'" H51 sing N N 27 1AP "C4'" "O4'" sing N N 28 1AP "C4'" "C3'" sing N N 29 1AP "C4'" H4 sing N N 30 1AP "O4'" "C1'" sing N N 31 1AP "C1'" "C2'" sing N N 32 1AP "C1'" H11 sing N N 33 1AP "C2'" "C3'" sing N N 34 1AP "C2'" H21 sing N N 35 1AP "C2'" H22 sing N N 36 1AP "C3'" "O3'" sing N N 37 1AP "C3'" H31 sing N N 38 1AP "O3'" HO31 sing N N 39 1AP OP3 H3P 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 1S1K 'double helix' 1S1K 'b-form double helix' 1S1K '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 A DG 10 12_545 0.772 -0.507 -0.044 0.319 -0.481 -3.917 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 12_545 0.286 -0.077 0.246 -3.987 -8.813 -5.656 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A 1AP 3 1_555 A DT 8 12_545 0.131 0.006 -0.239 -4.157 -5.707 -2.518 3 A_1AP3:DT8_A A 3 ? A 8 ? ? ? 1 A DG 4 1_555 A DC 7 12_545 -0.331 -0.017 0.212 -1.850 -11.463 -3.866 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DT 5 1_555 A DA 6 12_545 -0.171 -0.178 0.330 -1.504 -11.056 -2.231 5 A_DT5:DA6_A A 5 ? A 6 ? 20 1 1 A DA 6 1_555 A DT 5 12_545 0.171 -0.178 0.330 1.504 -11.056 -2.231 6 A_DA6:DT5_A A 6 ? A 5 ? 20 1 1 A DC 7 1_555 A DG 4 12_545 0.331 -0.017 0.212 1.850 -11.463 -3.866 7 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DT 8 1_555 A 1AP 3 12_545 -0.131 0.006 -0.239 4.157 -5.707 -2.518 8 A_DT8:1AP3_A A 8 ? A 3 ? ? ? 1 A DG 9 1_555 A DC 2 12_545 -0.286 -0.077 0.246 3.987 -8.813 -5.656 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 12_545 -0.772 -0.507 -0.044 -0.319 -0.481 -3.917 10 A_DG10:DC1_A A 10 ? A 1 ? 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 A DG 10 12_545 A DC 2 1_555 A DG 9 12_545 -0.392 0.060 3.403 1.394 7.566 33.233 -1.148 0.900 3.317 13.012 -2.398 34.087 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 12_545 A 1AP 3 1_555 A DT 8 12_545 0.231 0.780 3.398 4.349 8.156 39.026 0.143 0.193 3.491 12.005 -6.402 40.064 2 AA_DC21AP3:DT8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A 1AP 3 1_555 A DT 8 12_545 A DG 4 1_555 A DC 7 12_545 0.533 -0.116 3.243 -4.180 2.881 31.633 -0.719 -1.705 3.126 5.242 7.607 32.028 3 AA_1AP3DG4:DC7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 12_545 A DT 5 1_555 A DA 6 12_545 -0.021 -0.755 3.351 -2.195 3.072 29.059 -2.164 -0.439 3.248 6.090 4.350 29.298 4 AA_DG4DT5:DA6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DT 5 1_555 A DA 6 12_545 A DA 6 1_555 A DT 5 12_545 0.000 0.368 3.246 0.000 2.834 45.629 0.228 0.000 3.262 3.650 0.000 45.713 5 AA_DT5DA6:DT5DA6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DA 6 1_555 A DT 5 12_545 A DC 7 1_555 A DG 4 12_545 0.021 -0.755 3.351 2.195 3.072 29.059 -2.164 0.439 3.248 6.090 -4.350 29.298 6 AA_DA6DC7:DG4DT5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 12_545 A DT 8 1_555 A 1AP 3 12_545 -0.533 -0.116 3.243 4.180 2.881 31.633 -0.719 1.705 3.126 5.242 -7.607 32.028 7 AA_DC7DT8:1AP3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DT 8 1_555 A 1AP 3 12_545 A DG 9 1_555 A DC 2 12_545 -0.231 0.780 3.398 -4.349 8.156 39.026 0.143 -0.193 3.491 12.005 6.402 40.064 8 AA_DT8DG9:DC21AP3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 12_545 A DG 10 1_555 A DC 1 12_545 0.392 0.060 3.403 -1.394 7.566 33.233 -1.148 -0.900 3.317 13.012 2.398 34.087 9 AA_DG9DG10:DC1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 'SODIUM ION' NA 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1P4Z _pdbx_initial_refinement_model.details ? #