data_3QK4 # _entry.id 3QK4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 3QK4 pdb_00003qk4 10.2210/pdb3qk4/pdb NDB NA0937 ? ? RCSB RCSB063745 ? ? WWPDB D_1000063745 ? ? # 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 2011-03-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-03-20 4 'Structure model' 1 3 2024-04-03 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3QK4 _pdbx_database_status.recvd_initial_deposition_date 2011-01-31 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Venkadesh, S.' 1 'Mandal, P.K.' 2 'Gautham, N.' 3 # _citation.id primary _citation.title 'The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2)' _citation.journal_abbrev Biochem.Biophys.Res.Commun. _citation.journal_volume 407 _citation.page_first 307 _citation.page_last 312 _citation.year 2011 _citation.journal_id_ASTM BBRCA9 _citation.country US _citation.journal_id_ISSN 0006-291X _citation.journal_id_CSD 0146 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21397589 _citation.pdbx_database_id_DOI 10.1016/j.bbrc.2011.03.007 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Venkadesh, S.' 1 ? primary 'Mandal, P.K.' 2 ? primary 'Gautham, N.' 3 ? # 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*GP*GP*TP*AP*CP*CP*CP*GP*CP*G)-3') ; 4282.768 2 ? ? ? ? 2 water nat water 18.015 46 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGGGTACCCGCG _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 DG n 1 6 DG n 1 7 DT n 1 8 DA n 1 9 DC n 1 10 DC n 1 11 DC n 1 12 DG n 1 13 DC n 1 14 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # 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 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DC 13 13 13 DC DC A . n A 1 14 DG 14 14 14 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DG 4 4 4 DG DG B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 DG 6 6 6 DG DG B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DA 8 8 8 DA DA B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DC 10 10 10 DC DC B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DG 12 12 12 DG DG B . n B 1 13 DC 13 13 13 DC DC B . n B 1 14 DG 14 14 14 DG DG 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 15 15 HOH HOH A . C 2 HOH 2 16 16 HOH HOH A . C 2 HOH 3 17 17 HOH HOH A . C 2 HOH 4 18 18 HOH HOH A . C 2 HOH 5 19 1 HOH HOH A . C 2 HOH 6 20 3 HOH HOH A . C 2 HOH 7 21 6 HOH HOH A . C 2 HOH 8 22 5 HOH HOH A . C 2 HOH 9 23 8 HOH HOH A . C 2 HOH 10 24 24 HOH HOH A . C 2 HOH 11 25 10 HOH HOH A . C 2 HOH 12 26 13 HOH HOH A . C 2 HOH 13 27 27 HOH HOH A . C 2 HOH 14 28 12 HOH HOH A . C 2 HOH 15 29 29 HOH HOH A . C 2 HOH 16 31 31 HOH HOH A . C 2 HOH 17 32 32 HOH HOH A . C 2 HOH 18 36 36 HOH HOH A . C 2 HOH 19 37 37 HOH HOH A . C 2 HOH 20 38 38 HOH HOH A . C 2 HOH 21 39 39 HOH HOH A . C 2 HOH 22 40 40 HOH HOH A . C 2 HOH 23 41 41 HOH HOH A . C 2 HOH 24 45 45 HOH HOH A . D 2 HOH 1 15 2 HOH HOH B . D 2 HOH 2 16 4 HOH HOH B . D 2 HOH 3 18 7 HOH HOH B . D 2 HOH 4 19 19 HOH HOH B . D 2 HOH 5 20 20 HOH HOH B . D 2 HOH 6 21 21 HOH HOH B . D 2 HOH 7 22 22 HOH HOH B . D 2 HOH 8 23 23 HOH HOH B . D 2 HOH 9 24 11 HOH HOH B . D 2 HOH 10 25 25 HOH HOH B . D 2 HOH 11 26 26 HOH HOH B . D 2 HOH 12 27 9 HOH HOH B . D 2 HOH 13 28 14 HOH HOH B . D 2 HOH 14 29 28 HOH HOH B . D 2 HOH 15 30 30 HOH HOH B . D 2 HOH 16 33 33 HOH HOH B . D 2 HOH 17 34 34 HOH HOH B . D 2 HOH 18 35 35 HOH HOH B . D 2 HOH 19 42 42 HOH HOH B . D 2 HOH 20 43 43 HOH HOH B . D 2 HOH 21 44 44 HOH HOH B . D 2 HOH 22 46 46 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 AMoRE phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 AUTOMAR 'data reduction' . ? 4 # _cell.entry_id 3QK4 _cell.length_a 28.988 _cell.length_b 28.988 _cell.length_c 87.662 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3QK4 _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3QK4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.79 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.99 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;The drop consist of 1mM DNA, 50mM buffer, 10mM BaCl2, 1mM Spermine equilibriated against 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 300K ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2008-12-17 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator Mirrors _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54179 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'BRUKER AXS MICROSTAR' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.54179 # _reflns.entry_id 3QK4 _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 2.60 _reflns.number_obs 2171 _reflns.number_all 2256 _reflns.percent_possible_obs 96.20 _reflns.pdbx_Rmerge_I_obs 0.0770 _reflns.pdbx_Rsym_value 0.0714 _reflns.pdbx_netI_over_sigmaI 4.50 _reflns.B_iso_Wilson_estimate 57.76 _reflns.pdbx_redundancy 3.67 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.69 _reflns_shell.percent_possible_all 95.4 _reflns_shell.Rmerge_I_obs 0.4184 _reflns_shell.pdbx_Rsym_value 0.3936 _reflns_shell.meanI_over_sigI_obs 1.2 _reflns_shell.pdbx_redundancy 3.71 _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3QK4 _refine.ls_number_reflns_obs 2042 _refine.ls_number_reflns_all 2168 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.96 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 97.18 _refine.ls_R_factor_obs 0.24734 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.24580 _refine.ls_R_factor_R_free 0.27440 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.8 _refine.ls_number_reflns_R_free 126 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.902 _refine.correlation_coeff_Fo_to_Fc_free 0.866 _refine.B_iso_mean 43.531 _refine.aniso_B[1][1] 18.22 _refine.aniso_B[2][2] 18.22 _refine.aniso_B[3][3] -36.44 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'A-DNA fiber Model' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.244 _refine.pdbx_overall_ESU_R_Free 0.085 _refine.overall_SU_ML 0.297 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 14.130 _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.ls_redundancy_reflns_obs ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? # _refine_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 568 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 46 _refine_hist.number_atoms_total 614 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 19.96 # 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 r_bond_refined_d 0.023 0.021 ? 636 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.975 3.000 ? 978 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.152 0.200 ? 110 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 294 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.602 _refine_ls_shell.d_res_low 2.669 _refine_ls_shell.number_reflns_R_work 141 _refine_ls_shell.R_factor_R_work 0.443 _refine_ls_shell.percent_reflns_obs 94.74 _refine_ls_shell.R_factor_R_free 0.394 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 3 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _database_PDB_matrix.entry_id 3QK4 _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 3QK4 _struct.title 'Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QK4 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA duplex, 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.db_name PDB _struct_ref.db_code 3QK4 _struct_ref.pdbx_db_accession 3QK4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3QK4 A 1 ? 14 ? 3QK4 1 ? 14 ? 1 14 2 1 3QK4 B 1 ? 14 ? 3QK4 1 ? 14 ? 1 14 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1450 ? 1 MORE -1 ? 1 'SSA (A^2)' 5230 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 14 N1 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 14 O6 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 14 N2 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 13 O2 ? ? A DG 2 B DC 13 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog5 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 4 B DC 11 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DG 12 O6 ? ? A DG 4 B DG 12 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog10 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 6 B DC 9 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog19 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog20 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog27 hydrog ? ? B DT 7 N3 ? ? ? 1_555 B DA 8 N7 ? ? B DT 7 B DA 8 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 1.566 1.512 0.054 0.007 N 2 1 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.581 1.435 0.146 0.013 N 3 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.567 1.512 0.055 0.007 N 4 1 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 1.559 1.512 0.047 0.007 N 5 1 N3 A DG 6 ? ? C4 A DG 6 ? ? 1.392 1.350 0.042 0.007 N 6 1 N9 A DG 6 ? ? C4 A DG 6 ? ? 1.434 1.375 0.059 0.008 N 7 1 N9 A DA 8 ? ? C4 A DA 8 ? ? 1.415 1.374 0.041 0.006 N 8 1 N1 A DC 11 ? ? C6 A DC 11 ? ? 1.406 1.367 0.039 0.006 N 9 1 N3 A DC 11 ? ? C4 A DC 11 ? ? 1.380 1.335 0.045 0.007 N 10 1 N9 A DG 12 ? ? C4 A DG 12 ? ? 1.445 1.375 0.070 0.008 N 11 1 "C5'" B DC 3 ? ? "C4'" B DC 3 ? ? 1.565 1.512 0.053 0.007 N 12 1 "C5'" B DG 5 ? ? "C4'" B DG 5 ? ? 1.563 1.512 0.051 0.007 N 13 1 "O3'" B DG 6 ? ? "C3'" B DG 6 ? ? 1.517 1.435 0.082 0.013 N 14 1 "C1'" B DC 13 ? ? N1 B DC 13 ? ? 1.566 1.488 0.078 0.013 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 ? ? "C2'" A DC 1 ? ? 100.26 105.90 -5.64 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.42 108.30 4.12 0.30 N 3 1 "C3'" A DC 1 ? ? "O3'" A DC 1 ? ? P A DG 2 ? ? 136.55 119.70 16.85 1.20 Y 4 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 98.49 104.50 -6.01 0.40 N 5 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 123.33 115.70 7.63 1.20 N 6 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? "O4'" A DG 2 ? ? 117.40 109.80 7.60 1.10 N 7 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 95.76 102.20 -6.44 0.70 N 8 1 N3 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 125.48 128.60 -3.12 0.50 N 9 1 N3 A DG 2 ? ? C4 A DG 2 ? ? N9 A DG 2 ? ? 130.52 126.00 4.52 0.60 N 10 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 101.32 104.50 -3.18 0.40 N 11 1 "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? 94.63 102.20 -7.57 0.70 N 12 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 113.49 108.30 5.19 0.30 N 13 1 N7 A DG 4 ? ? C8 A DG 4 ? ? N9 A DG 4 ? ? 116.43 113.10 3.33 0.50 N 14 1 C8 A DG 4 ? ? N9 A DG 4 ? ? C4 A DG 4 ? ? 103.72 106.40 -2.68 0.40 N 15 1 "C3'" A DG 4 ? ? "O3'" A DG 4 ? ? P A DG 5 ? ? 128.48 119.70 8.78 1.20 Y 16 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? "C2'" A DG 5 ? ? 111.25 106.80 4.45 0.50 N 17 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 117.12 108.30 8.82 0.30 N 18 1 N9 A DG 5 ? ? C4 A DG 5 ? ? C5 A DG 5 ? ? 108.96 105.40 3.56 0.40 N 19 1 N3 A DG 5 ? ? C4 A DG 5 ? ? N9 A DG 5 ? ? 119.99 126.00 -6.01 0.60 N 20 1 N1 A DG 5 ? ? C2 A DG 5 ? ? N2 A DG 5 ? ? 122.80 116.20 6.60 0.90 N 21 1 N3 A DG 5 ? ? C2 A DG 5 ? ? N2 A DG 5 ? ? 113.60 119.90 -6.30 0.70 N 22 1 C8 A DG 5 ? ? N9 A DG 5 ? ? "C1'" A DG 5 ? ? 134.99 127.00 7.99 1.30 N 23 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 98.26 104.50 -6.24 0.40 N 24 1 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? "O4'" A DG 6 ? ? 119.40 109.80 9.60 1.10 N 25 1 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 95.21 102.20 -6.99 0.70 N 26 1 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? "C1'" A DG 6 ? ? 97.55 102.40 -4.85 0.80 N 27 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? "C2'" A DG 6 ? ? 99.41 105.90 -6.49 0.80 N 28 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 112.88 108.30 4.58 0.30 N 29 1 N3 A DG 6 ? ? C4 A DG 6 ? ? C5 A DG 6 ? ? 122.51 128.60 -6.09 0.50 N 30 1 C4 A DG 6 ? ? C5 A DG 6 ? ? C6 A DG 6 ? ? 124.30 118.80 5.50 0.60 N 31 1 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.90 113.10 3.80 0.50 N 32 1 C8 A DG 6 ? ? N9 A DG 6 ? ? C4 A DG 6 ? ? 103.96 106.40 -2.44 0.40 N 33 1 N3 A DG 6 ? ? C4 A DG 6 ? ? N9 A DG 6 ? ? 134.33 126.00 8.33 0.60 N 34 1 C6 A DG 6 ? ? C5 A DG 6 ? ? N7 A DG 6 ? ? 122.90 130.40 -7.50 0.60 N 35 1 C8 A DG 6 ? ? N9 A DG 6 ? ? "C1'" A DG 6 ? ? 115.23 127.00 -11.77 1.30 N 36 1 C4 A DG 6 ? ? N9 A DG 6 ? ? "C1'" A DG 6 ? ? 140.81 126.50 14.31 1.30 N 37 1 "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? "C3'" A DT 7 ? ? 96.04 104.50 -8.46 0.40 N 38 1 "C3'" A DT 7 ? ? "C2'" A DT 7 ? ? "C1'" A DT 7 ? ? 92.98 102.40 -9.42 0.80 N 39 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 100.62 105.90 -5.28 0.80 N 40 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 126.09 119.90 6.19 0.60 N 41 1 C5 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 120.27 124.90 -4.63 0.70 N 42 1 "C4'" A DA 8 ? ? "C3'" A DA 8 ? ? "C2'" A DA 8 ? ? 93.69 102.20 -8.51 0.70 N 43 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? "C2'" A DA 8 ? ? 99.09 105.90 -6.81 0.80 N 44 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 119.92 108.30 11.62 0.30 N 45 1 C2 A DA 8 ? ? N3 A DA 8 ? ? C4 A DA 8 ? ? 114.72 110.60 4.12 0.50 N 46 1 C8 A DA 8 ? ? N9 A DA 8 ? ? "C1'" A DA 8 ? ? 116.43 127.70 -11.27 1.80 N 47 1 C4 A DA 8 ? ? N9 A DA 8 ? ? "C1'" A DA 8 ? ? 139.24 126.30 12.94 1.80 N 48 1 C5 A DC 9 ? ? C6 A DC 9 ? ? N1 A DC 9 ? ? 124.70 121.00 3.70 0.50 N 49 1 C5 A DC 9 ? ? C4 A DC 9 ? ? N4 A DC 9 ? ? 115.44 120.20 -4.76 0.70 N 50 1 C2 A DC 9 ? ? N1 A DC 9 ? ? "C1'" A DC 9 ? ? 125.48 118.80 6.68 1.10 N 51 1 "C3'" A DC 9 ? ? "O3'" A DC 9 ? ? P A DC 10 ? ? 107.56 119.70 -12.14 1.20 Y 52 1 "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? 100.71 104.50 -3.79 0.40 N 53 1 "C3'" A DC 10 ? ? "C2'" A DC 10 ? ? "C1'" A DC 10 ? ? 96.14 102.40 -6.26 0.80 N 54 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? "C2'" A DC 10 ? ? 100.62 105.90 -5.28 0.80 N 55 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 113.99 108.30 5.69 0.30 N 56 1 "C3'" A DC 10 ? ? "O3'" A DC 10 ? ? P A DC 11 ? ? 107.00 119.70 -12.70 1.20 Y 57 1 "O5'" A DC 11 ? ? P A DC 11 ? ? OP2 A DC 11 ? ? 99.11 105.70 -6.59 0.90 N 58 1 "O5'" A DC 11 ? ? "C5'" A DC 11 ? ? "C4'" A DC 11 ? ? 102.63 109.40 -6.77 0.80 N 59 1 "O4'" A DC 11 ? ? "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? 92.11 104.50 -12.39 0.40 N 60 1 "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? "C2'" A DC 11 ? ? 89.86 102.20 -12.34 0.70 N 61 1 "C3'" A DC 11 ? ? "C2'" A DC 11 ? ? "C1'" A DC 11 ? ? 96.08 102.40 -6.32 0.80 N 62 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? "C2'" A DC 11 ? ? 100.88 105.90 -5.02 0.80 N 63 1 N1 A DC 11 ? ? C2 A DC 11 ? ? N3 A DC 11 ? ? 114.27 119.20 -4.93 0.70 N 64 1 C2 A DC 11 ? ? N3 A DC 11 ? ? C4 A DC 11 ? ? 124.88 119.90 4.98 0.50 N 65 1 C4 A DC 11 ? ? C5 A DC 11 ? ? C6 A DC 11 ? ? 111.80 117.40 -5.60 0.50 N 66 1 C5 A DC 11 ? ? C6 A DC 11 ? ? N1 A DC 11 ? ? 127.56 121.00 6.56 0.50 N 67 1 N3 A DC 11 ? ? C4 A DC 11 ? ? N4 A DC 11 ? ? 124.81 118.00 6.81 0.70 N 68 1 C5 A DC 11 ? ? C4 A DC 11 ? ? N4 A DC 11 ? ? 112.64 120.20 -7.56 0.70 N 69 1 "C3'" A DC 11 ? ? "O3'" A DC 11 ? ? P A DG 12 ? ? 127.85 119.70 8.15 1.20 Y 70 1 "O3'" A DC 11 ? ? P A DG 12 ? ? "O5'" A DG 12 ? ? 91.92 104.00 -12.08 1.90 Y 71 1 "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? 102.02 104.50 -2.48 0.40 N 72 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.64 108.30 2.34 0.30 N 73 1 C6 A DG 12 ? ? N1 A DG 12 ? ? C2 A DG 12 ? ? 120.58 125.10 -4.52 0.60 N 74 1 C2 A DG 12 ? ? N3 A DG 12 ? ? C4 A DG 12 ? ? 116.42 111.90 4.52 0.50 N 75 1 N3 A DG 12 ? ? C4 A DG 12 ? ? C5 A DG 12 ? ? 120.67 128.60 -7.93 0.50 N 76 1 C5 A DG 12 ? ? C6 A DG 12 ? ? N1 A DG 12 ? ? 115.82 111.50 4.32 0.50 N 77 1 C4 A DG 12 ? ? C5 A DG 12 ? ? N7 A DG 12 ? ? 108.08 110.80 -2.72 0.40 N 78 1 N7 A DG 12 ? ? C8 A DG 12 ? ? N9 A DG 12 ? ? 116.49 113.10 3.39 0.50 N 79 1 C8 A DG 12 ? ? N9 A DG 12 ? ? C4 A DG 12 ? ? 101.77 106.40 -4.63 0.40 N 80 1 N9 A DG 12 ? ? C4 A DG 12 ? ? C5 A DG 12 ? ? 107.97 105.40 2.57 0.40 N 81 1 N3 A DG 12 ? ? C4 A DG 12 ? ? N9 A DG 12 ? ? 131.36 126.00 5.36 0.60 N 82 1 N1 A DG 12 ? ? C6 A DG 12 ? ? O6 A DG 12 ? ? 113.29 119.90 -6.61 0.60 N 83 1 C4 A DG 12 ? ? N9 A DG 12 ? ? "C1'" A DG 12 ? ? 136.70 126.50 10.20 1.30 N 84 1 "O4'" A DC 13 ? ? "C1'" A DC 13 ? ? N1 A DC 13 ? ? 97.12 108.00 -10.88 0.70 N 85 1 C4 A DC 13 ? ? C5 A DC 13 ? ? C6 A DC 13 ? ? 113.96 117.40 -3.44 0.50 N 86 1 "O4'" A DG 14 ? ? "C1'" A DG 14 ? ? "C2'" A DG 14 ? ? 99.67 105.90 -6.23 0.80 N 87 1 "O5'" B DC 1 ? ? "C5'" B DC 1 ? ? "C4'" B DC 1 ? ? 101.91 109.40 -7.49 0.80 N 88 1 "C1'" B DC 1 ? ? "O4'" B DC 1 ? ? "C4'" B DC 1 ? ? 102.22 110.10 -7.88 1.00 N 89 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? "C2'" B DC 1 ? ? 99.80 105.90 -6.10 0.80 N 90 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 119.37 108.30 11.07 0.30 N 91 1 C6 B DC 1 ? ? N1 B DC 1 ? ? C2 B DC 1 ? ? 117.67 120.30 -2.63 0.40 N 92 1 C5 B DC 1 ? ? C4 B DC 1 ? ? N4 B DC 1 ? ? 125.03 120.20 4.83 0.70 N 93 1 "C3'" B DC 1 ? ? "O3'" B DC 1 ? ? P B DG 2 ? ? 129.74 119.70 10.04 1.20 Y 94 1 "C5'" B DG 2 ? ? "C4'" B DG 2 ? ? "O4'" B DG 2 ? ? 116.74 109.80 6.94 1.10 N 95 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? N9 B DG 2 ? ? 102.50 108.00 -5.50 0.70 N 96 1 "O5'" B DC 3 ? ? P B DC 3 ? ? OP2 B DC 3 ? ? 120.69 110.70 9.99 1.20 N 97 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? "C2'" B DC 3 ? ? 110.02 106.80 3.22 0.50 N 98 1 C5 B DC 3 ? ? C4 B DC 3 ? ? N4 B DC 3 ? ? 115.93 120.20 -4.27 0.70 N 99 1 "C1'" B DG 4 ? ? "O4'" B DG 4 ? ? "C4'" B DG 4 ? ? 103.82 110.10 -6.28 1.00 N 100 1 "C3'" B DG 4 ? ? "C2'" B DG 4 ? ? "C1'" B DG 4 ? ? 97.59 102.40 -4.81 0.80 N 101 1 "O4'" B DG 4 ? ? "C1'" B DG 4 ? ? N9 B DG 4 ? ? 122.38 108.30 14.08 0.30 N 102 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 112.49 108.30 4.19 0.30 N 103 1 "C1'" B DG 6 ? ? "O4'" B DG 6 ? ? "C4'" B DG 6 ? ? 114.70 110.30 4.40 0.70 N 104 1 "C3'" B DG 6 ? ? "C2'" B DG 6 ? ? "C1'" B DG 6 ? ? 112.27 102.50 9.77 1.20 N 105 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? "C2'" B DG 6 ? ? 100.60 105.90 -5.30 0.80 N 106 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 114.12 108.30 5.82 0.30 N 107 1 C6 B DG 6 ? ? N1 B DG 6 ? ? C2 B DG 6 ? ? 120.55 125.10 -4.55 0.60 N 108 1 C2 B DG 6 ? ? N3 B DG 6 ? ? C4 B DG 6 ? ? 115.12 111.90 3.22 0.50 N 109 1 C5 B DG 6 ? ? C6 B DG 6 ? ? N1 B DG 6 ? ? 114.85 111.50 3.35 0.50 N 110 1 N7 B DG 6 ? ? C8 B DG 6 ? ? N9 B DG 6 ? ? 116.37 113.10 3.27 0.50 N 111 1 C8 B DG 6 ? ? N9 B DG 6 ? ? C4 B DG 6 ? ? 101.93 106.40 -4.47 0.40 N 112 1 N9 B DG 6 ? ? C4 B DG 6 ? ? C5 B DG 6 ? ? 108.87 105.40 3.47 0.40 N 113 1 N3 B DG 6 ? ? C2 B DG 6 ? ? N2 B DG 6 ? ? 114.52 119.90 -5.38 0.70 N 114 1 N1 B DG 6 ? ? C6 B DG 6 ? ? O6 B DG 6 ? ? 116.04 119.90 -3.86 0.60 N 115 1 "C3'" B DG 6 ? ? "O3'" B DG 6 ? ? P B DT 7 ? ? 130.50 119.70 10.80 1.20 Y 116 1 "O4'" B DT 7 ? ? "C4'" B DT 7 ? ? "C3'" B DT 7 ? ? 101.50 104.50 -3.00 0.40 N 117 1 "C3'" B DT 7 ? ? "C2'" B DT 7 ? ? "C1'" B DT 7 ? ? 93.00 102.40 -9.40 0.80 N 118 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 99.90 105.90 -6.00 0.80 N 119 1 C6 B DT 7 ? ? N1 B DT 7 ? ? C2 B DT 7 ? ? 118.23 121.30 -3.07 0.50 N 120 1 C5 B DT 7 ? ? C6 B DT 7 ? ? N1 B DT 7 ? ? 127.86 123.70 4.16 0.60 N 121 1 N1 B DT 7 ? ? C2 B DT 7 ? ? O2 B DT 7 ? ? 128.10 123.10 5.00 0.80 N 122 1 N3 B DT 7 ? ? C2 B DT 7 ? ? O2 B DT 7 ? ? 118.58 122.30 -3.72 0.60 N 123 1 N3 B DT 7 ? ? C4 B DT 7 ? ? O4 B DT 7 ? ? 123.93 119.90 4.03 0.60 N 124 1 C6 B DT 7 ? ? N1 B DT 7 ? ? "C1'" B DT 7 ? ? 135.58 120.40 15.18 1.50 N 125 1 C2 B DT 7 ? ? N1 B DT 7 ? ? "C1'" B DT 7 ? ? 106.11 118.20 -12.09 1.60 N 126 1 P B DA 8 ? ? "O5'" B DA 8 ? ? "C5'" B DA 8 ? ? 109.89 120.90 -11.01 1.60 N 127 1 C2 B DA 8 ? ? N3 B DA 8 ? ? C4 B DA 8 ? ? 114.02 110.60 3.42 0.50 N 128 1 "C5'" B DC 9 ? ? "C4'" B DC 9 ? ? "C3'" B DC 9 ? ? 102.38 114.10 -11.72 1.80 N 129 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 99.29 105.90 -6.61 0.80 N 130 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 116.36 108.30 8.06 0.30 N 131 1 C6 B DC 9 ? ? N1 B DC 9 ? ? C2 B DC 9 ? ? 117.16 120.30 -3.14 0.40 N 132 1 C5 B DC 9 ? ? C6 B DC 9 ? ? N1 B DC 9 ? ? 124.74 121.00 3.74 0.50 N 133 1 N3 B DC 9 ? ? C4 B DC 9 ? ? N4 B DC 9 ? ? 123.75 118.00 5.75 0.70 N 134 1 C5 B DC 9 ? ? C4 B DC 9 ? ? N4 B DC 9 ? ? 114.55 120.20 -5.65 0.70 N 135 1 "C3'" B DC 10 ? ? "O3'" B DC 10 ? ? P B DC 11 ? ? 112.22 119.70 -7.48 1.20 Y 136 1 "O3'" B DC 10 ? ? P B DC 11 ? ? OP1 B DC 11 ? ? 117.14 110.50 6.64 1.10 Y 137 1 "C3'" B DC 11 ? ? "O3'" B DC 11 ? ? P B DG 12 ? ? 127.85 119.70 8.15 1.20 Y 138 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 102.09 104.50 -2.41 0.40 N 139 1 "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 124.20 115.70 8.50 1.20 N 140 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.38 108.30 2.08 0.30 N 141 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 117.39 108.30 9.09 0.30 N 142 1 C6 B DC 13 ? ? N1 B DC 13 ? ? C2 B DC 13 ? ? 117.61 120.30 -2.69 0.40 N 143 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P B DG 14 ? ? 127.88 119.70 8.18 1.20 Y 144 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 111.35 108.30 3.05 0.30 N # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3QK4 'double helix' 3QK4 'a-form double helix' 3QK4 '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 14 1_555 0.398 -0.888 -2.160 16.056 26.865 -14.458 1 A_DC1:DG14_B A 1 ? B 14 ? 19 1 1 A DG 2 1_555 B DC 13 1_555 -1.024 -0.378 -0.275 -16.873 -6.820 -18.087 2 A_DG2:DC13_B A 2 ? B 13 ? ? 1 1 A DC 3 1_555 B DG 12 1_555 -0.050 0.270 -0.887 -8.672 3.866 -0.255 3 A_DC3:DG12_B A 3 ? B 12 ? 19 1 1 A DG 4 1_555 B DC 11 1_555 -0.330 0.539 1.193 17.705 -13.237 19.649 4 A_DG4:DC11_B A 4 ? B 11 ? ? 1 1 A DG 5 1_555 B DC 10 1_555 0.455 -0.347 1.443 23.306 -26.081 5.205 5 A_DG5:DC10_B A 5 ? B 10 ? 19 1 1 A DG 6 1_555 B DC 9 1_555 0.152 0.721 -0.413 -15.281 -14.629 -20.017 6 A_DG6:DC9_B A 6 ? B 9 ? ? ? 1 A DT 7 1_555 B DA 8 1_555 -0.330 0.185 -0.345 -7.247 -14.893 -28.587 7 A_DT7:DA8_B A 7 ? B 8 ? 20 1 1 A DC 9 1_555 B DG 6 1_555 -0.017 -0.347 0.764 4.163 -7.810 -21.712 8 A_DC9:DG6_B A 9 ? B 6 ? ? 1 1 A DC 10 1_555 B DG 5 1_555 -0.268 -0.060 0.242 2.159 -22.368 -24.750 9 A_DC10:DG5_B A 10 ? B 5 ? ? 1 1 A DG 12 1_555 B DC 3 1_555 0.149 0.237 -0.442 -5.891 -19.802 -3.714 10 A_DG12:DC3_B A 12 ? B 3 ? 19 1 1 A DC 13 1_555 B DG 2 1_555 0.139 0.063 -0.446 12.187 -10.008 -10.311 11 A_DC13:DG2_B A 13 ? B 2 ? 19 1 1 A DG 14 1_555 B DC 1 1_555 -0.115 0.434 0.668 3.829 15.506 0.206 12 A_DG14:DC1_B A 14 ? B 1 ? ? 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 14 1_555 A DG 2 1_555 B DC 13 1_555 -0.387 -0.924 4.421 -8.016 34.457 54.684 -2.812 -0.089 3.400 33.870 7.879 64.381 1 AA_DC1DG2:DC13DG14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A DG 2 1_555 B DC 13 1_555 A DC 3 1_555 B DG 12 1_555 -0.349 -3.235 3.104 10.423 2.735 12.974 -12.523 6.840 1.655 10.115 -38.552 16.851 2 AA_DG2DC3:DG12DC13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A DC 3 1_555 B DG 12 1_555 A DG 4 1_555 B DC 11 1_555 2.635 -0.152 1.626 -8.075 20.179 38.272 -1.000 -3.850 0.894 28.182 11.277 43.811 3 AA_DC3DG4:DC11DG12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A DG 4 1_555 B DC 11 1_555 A DG 5 1_555 B DC 10 1_555 -0.071 -2.249 3.408 7.124 8.219 22.537 -7.458 2.124 2.328 19.629 -17.012 24.994 4 AA_DG4DG5:DC10DC11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A DG 5 1_555 B DC 10 1_555 A DG 6 1_555 B DC 9 1_555 -2.843 -1.380 4.361 6.765 7.483 40.578 -2.903 4.863 3.565 10.593 -9.576 41.762 5 AA_DG5DG6:DC9DC10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A DG 6 1_555 B DC 9 1_555 A DT 7 1_555 B DA 8 1_555 -1.372 -1.638 3.024 -6.814 14.446 25.223 -5.755 1.457 2.096 29.595 13.960 29.786 6 AA_DG6DT7:DA8DC9_BB A 6 ? B 9 ? A 7 ? B 8 ? 1 A DC 9 1_555 B DG 6 1_555 A DC 10 1_555 B DG 5 1_555 -0.446 -2.829 2.999 -0.874 -1.536 33.667 -4.644 0.636 3.131 -2.649 1.508 33.712 7 AA_DC9DC10:DG5DG6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A DG 12 1_555 B DC 3 1_555 A DC 13 1_555 B DG 2 1_555 1.029 -1.174 3.363 -4.400 -0.752 13.788 -3.991 -7.957 2.950 -3.030 17.732 14.489 8 AA_DG12DC13:DG2DC3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DC 13 1_555 B DG 2 1_555 A DG 14 1_555 B DC 1 1_555 2.626 -0.940 2.800 3.015 7.127 50.676 -1.510 -2.859 2.794 8.271 -3.499 51.225 9 AA_DC13DG14:DC1DG2_BB A 13 ? B 2 ? A 14 ? B 1 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'A-DNA fiber Model' # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.673 2 1 1 ? '-H, K, -L' 0.327 # _atom_sites.entry_id 3QK4 _atom_sites.fract_transf_matrix[1][1] 0.034497 _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] 0.034497 _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] 0.011407 _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_