data_4QKK # _entry.id 4QKK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 4QKK pdb_00004qkk 10.2210/pdb4qkk/pdb NDB NA3051 ? ? RCSB RCSB086171 ? ? WWPDB D_1000086171 ? ? # 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 2014-12-10 2 'Structure model' 1 1 2019-12-25 3 'Structure model' 1 2 2024-03-20 # _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' 'Database references' 2 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Source and taxonomy' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 2 'Structure model' pdbx_entity_src_syn 4 2 'Structure model' struct_conn 5 3 'Structure model' chem_comp_atom 6 3 'Structure model' chem_comp_bond 7 3 'Structure model' database_2 # 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 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.pdbx_database_id_PubMed' 5 2 'Structure model' '_citation.year' 6 2 'Structure model' '_citation_author.name' 7 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_database_2.pdbx_DOI' 9 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4QKK _pdbx_database_status.recvd_initial_deposition_date 2014-06-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Raiber, E.-A.' 1 'Murat, P.' 2 'Chirgadze, D.Y.' 3 'Luisi, B.F.' 4 'Balasubramanian, S.' 5 # _citation.id primary _citation.title '5-Formylcytosine alters the structure of the DNA double helix.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 22 _citation.page_first 44 _citation.page_last 49 _citation.year 2015 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9985 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25504322 _citation.pdbx_database_id_DOI 10.1038/nsmb.2936 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Raiber, E.A.' 1 ? primary 'Murat, P.' 2 ? primary 'Chirgadze, D.Y.' 3 ? primary 'Beraldi, D.' 4 ? primary 'Luisi, B.F.' 5 ? primary 'Balasubramanian, S.' 6 ? # 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*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3') ; 3747.422 1 ? ? ? ? 2 water nat water 18.015 54 ? ? ? ? # _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)(DT)(DA)(5FC)(DG)(5FC)(DG)(5FC)(DG)(DT)(DA)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CTACGCGCGTAG _entity_poly.pdbx_strand_id A _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 DT n 1 3 DA n 1 4 5FC n 1 5 DG n 1 6 5FC n 1 7 DG n 1 8 5FC n 1 9 DG n 1 10 DT n 1 11 DA n 1 12 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 5FC 'DNA linking' n "5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" "2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE" 'C10 H14 N3 O8 P' 335.207 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 DT 2 2 2 DT DT A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 5FC 4 4 4 5FC 5FC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 5FC 6 6 6 5FC 5FC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 5FC 8 8 8 5FC 5FC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DA 11 11 11 DA DA A . n A 1 12 DG 12 12 12 DG DG 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 HOH 1 101 1 HOH HOH A . B 2 HOH 2 102 2 HOH HOH A . B 2 HOH 3 103 3 HOH HOH A . B 2 HOH 4 104 4 HOH HOH A . B 2 HOH 5 105 5 HOH HOH A . B 2 HOH 6 106 6 HOH HOH A . B 2 HOH 7 107 7 HOH HOH A . B 2 HOH 8 108 8 HOH HOH A . B 2 HOH 9 109 9 HOH HOH A . B 2 HOH 10 110 10 HOH HOH A . B 2 HOH 11 111 11 HOH HOH A . B 2 HOH 12 112 12 HOH HOH A . B 2 HOH 13 113 13 HOH HOH A . B 2 HOH 14 114 14 HOH HOH A . B 2 HOH 15 115 15 HOH HOH A . B 2 HOH 16 116 16 HOH HOH A . B 2 HOH 17 117 17 HOH HOH A . B 2 HOH 18 118 18 HOH HOH A . B 2 HOH 19 119 19 HOH HOH A . B 2 HOH 20 120 20 HOH HOH A . B 2 HOH 21 121 21 HOH HOH A . B 2 HOH 22 122 22 HOH HOH A . B 2 HOH 23 123 23 HOH HOH A . B 2 HOH 24 124 24 HOH HOH A . B 2 HOH 25 125 25 HOH HOH A . B 2 HOH 26 126 26 HOH HOH A . B 2 HOH 27 127 27 HOH HOH A . B 2 HOH 28 128 28 HOH HOH A . B 2 HOH 29 129 29 HOH HOH A . B 2 HOH 30 130 30 HOH HOH A . B 2 HOH 31 131 31 HOH HOH A . B 2 HOH 32 132 32 HOH HOH A . B 2 HOH 33 133 33 HOH HOH A . B 2 HOH 34 134 34 HOH HOH A . B 2 HOH 35 135 35 HOH HOH A . B 2 HOH 36 136 36 HOH HOH A . B 2 HOH 37 137 37 HOH HOH A . B 2 HOH 38 138 38 HOH HOH A . B 2 HOH 39 139 39 HOH HOH A . B 2 HOH 40 140 40 HOH HOH A . B 2 HOH 41 141 41 HOH HOH A . B 2 HOH 42 142 42 HOH HOH A . B 2 HOH 43 143 43 HOH HOH A . B 2 HOH 44 144 44 HOH HOH A . B 2 HOH 45 145 45 HOH HOH A . B 2 HOH 46 146 46 HOH HOH A . B 2 HOH 47 147 47 HOH HOH A . B 2 HOH 48 148 48 HOH HOH A . B 2 HOH 49 149 49 HOH HOH A . B 2 HOH 50 150 50 HOH HOH A . B 2 HOH 51 151 51 HOH HOH A . B 2 HOH 52 152 52 HOH HOH A . B 2 HOH 53 153 53 HOH HOH A . B 2 HOH 54 154 54 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal GDA 'data collection' . ? 1 PHENIX 'model building' '(phenix.refine: 1.9_1692)' ? 2 PHENIX refinement '(phenix.refine: 1.9_1692)' ? 3 XDS 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 PHENIX phasing 1.9_1692 ? 6 # _cell.entry_id 4QKK _cell.length_a 44.393 _cell.length_b 44.393 _cell.length_c 46.254 _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 4QKK _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4QKK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.04 _exptl_crystal.density_percent_sol 59.55 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '0.01M magnesium sulphate, 0.05M sodium cacodylate, 1.8M lithium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2014-04-17 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'double crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9686 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I24' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9686 # _reflns.entry_id 4QKK _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 46.25 _reflns.d_resolution_high 1.4 _reflns.number_obs 9608 _reflns.number_all 9608 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value 0.06 _reflns.pdbx_netI_over_sigmaI 19.3 _reflns.B_iso_Wilson_estimate 22.9 _reflns.pdbx_redundancy 12.1 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.48 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.1715 _reflns_shell.pdbx_Rsym_value 0.1715 _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_redundancy 12.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1347 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4QKK _refine.ls_number_reflns_obs 9567 _refine.ls_number_reflns_all 9567 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 25.974 _refine.ls_d_res_high 1.400 _refine.ls_percent_reflns_obs 99.99 _refine.ls_R_factor_obs 0.1411 _refine.ls_R_factor_all 0.1411 _refine.ls_R_factor_R_work 0.1401 _refine.ls_R_factor_R_free 0.1593 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.01 _refine.ls_number_reflns_R_free 479 _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 ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct P-SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.13 _refine.pdbx_overall_phase_error 27.42 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 249 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 54 _refine_hist.number_atoms_total 303 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 25.974 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.014 ? ? 278 ? 'X-RAY DIFFRACTION' f_angle_d 1.377 ? ? 427 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 23.801 ? ? 101 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.080 ? ? 44 ? 'X-RAY DIFFRACTION' f_plane_restr 0.011 ? ? 12 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs 'X-RAY DIFFRACTION' 3 1.4000 1.6026 2954 0.2104 100.00 0.2960 . . 152 . . . . 'X-RAY DIFFRACTION' 3 1.6026 2.0190 2986 0.1631 100.00 0.1650 . . 162 . . . . 'X-RAY DIFFRACTION' 3 2.0190 25.9784 3148 0.1288 100.00 0.1465 . . 165 . . . . # _database_PDB_matrix.entry_id 4QKK _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 4QKK _struct.title 'Crystal structure of an oligonucleotide containing 5-formylcytosine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4QKK _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Oligonucleotide, Epigenetic Ten-Eleven, Translocation proteins, Thymine DNA glycosylase, Formylcytosine, 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4QKK _struct_ref.pdbx_db_accession 4QKK _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4QKK _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4QKK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _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 12 # _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 # 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' 8_665 -y+1,-x+1,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 44.3930000000 -1.0000000000 0.0000000000 0.0000000000 44.3930000000 0.0000000000 0.0000000000 -1.0000000000 23.1270000000 # 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 DA 3 "O3'" ? ? ? 1_555 A 5FC 4 P ? ? A DA 3 A 5FC 4 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A 5FC 4 "O3'" ? ? ? 1_555 A DG 5 P ? ? A 5FC 4 A DG 5 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale3 covale both ? A DG 5 "O3'" ? ? ? 1_555 A 5FC 6 P ? ? A DG 5 A 5FC 6 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale4 covale both ? A 5FC 6 "O3'" ? ? ? 1_555 A DG 7 P ? ? A 5FC 6 A DG 7 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale5 covale both ? A DG 7 "O3'" ? ? ? 1_555 A 5FC 8 P ? ? A DG 7 A 5FC 8 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale6 covale both ? A 5FC 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A 5FC 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.611 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 12 N1 ? ? A DC 1 A DG 12 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 12 O6 ? ? A DC 1 A DG 12 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 12 N2 ? ? A DC 1 A DG 12 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 N3 ? ? ? 1_555 A DA 11 N1 ? ? A DT 2 A DA 11 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 2 O4 ? ? ? 1_555 A DA 11 N6 ? ? A DT 2 A DA 11 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 10 N3 ? ? A DA 3 A DT 10 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 10 O4 ? ? A DA 3 A DT 10 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 5FC 4 N3 ? ? ? 1_555 A DG 9 N1 ? ? A 5FC 4 A DG 9 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 5FC 4 N4 ? ? ? 1_555 A DG 9 O6 ? ? A 5FC 4 A DG 9 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 5FC 4 O2 ? ? ? 1_555 A DG 9 N2 ? ? A 5FC 4 A DG 9 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 A 5FC 8 N3 ? ? A DG 5 A 5FC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 A 5FC 8 O2 ? ? A DG 5 A 5FC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 A 5FC 8 N4 ? ? A DG 5 A 5FC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 5FC 6 N3 ? ? ? 1_555 A DG 7 N1 ? ? A 5FC 6 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 5FC 6 N4 ? ? ? 1_555 A DG 7 O6 ? ? A 5FC 6 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A 5FC 6 O2 ? ? ? 1_555 A DG 7 N2 ? ? A 5FC 6 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A 5FC 6 N3 ? ? A DG 7 A 5FC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A 5FC 6 O2 ? ? A DG 7 A 5FC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A 5FC 6 N4 ? ? A DG 7 A 5FC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 5FC 8 N3 ? ? ? 1_555 A DG 5 N1 ? ? A 5FC 8 A DG 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 5FC 8 N4 ? ? ? 1_555 A DG 5 O6 ? ? A 5FC 8 A DG 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 5FC 8 O2 ? ? ? 1_555 A DG 5 N2 ? ? A 5FC 8 A DG 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A 5FC 4 N3 ? ? A DG 9 A 5FC 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A 5FC 4 O2 ? ? A DG 9 A 5FC 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A 5FC 4 N4 ? ? A DG 9 A 5FC 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 10 A DA 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DT 10 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 10 A DA 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DA 11 N1 ? ? ? 1_555 A DT 2 N3 ? ? A DA 11 A DT 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DA 11 N6 ? ? ? 1_555 A DT 2 O4 ? ? A DA 11 A DT 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 12 A DC 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 12 A DC 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 12 A DC 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 "O3'" A DG 9 ? ? "C3'" A DG 9 ? ? 1.375 1.419 -0.044 0.006 N 2 1 "O3'" A DT 10 ? ? "C3'" A DT 10 ? ? 1.377 1.419 -0.042 0.006 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5FC 4 A 5FC 4 ? DC ? 2 A 5FC 6 A 5FC 6 ? DC ? 3 A 5FC 8 A 5FC 8 ? DC ? # 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 5FC P P N N 1 5FC OP2 O N N 2 5FC OP1 O N N 3 5FC "O5'" O N N 4 5FC N1 N N N 5 5FC C6 C N N 6 5FC C2 C N N 7 5FC O2 O N N 8 5FC N3 N N N 9 5FC C4 C N N 10 5FC N4 N N N 11 5FC C5 C N N 12 5FC "C2'" C N N 13 5FC "C5'" C N N 14 5FC "C4'" C N R 15 5FC "O4'" O N N 16 5FC "C1'" C N R 17 5FC "C3'" C N S 18 5FC "O3'" O N N 19 5FC C5A C N N 20 5FC O5A O N N 21 5FC OP3 O N N 22 5FC HOP2 H N N 23 5FC H6 H N N 24 5FC HN41 H N N 25 5FC HN42 H N N 26 5FC "H2'" H N N 27 5FC "H2''" H N N 28 5FC "H5'" H N N 29 5FC "H5''" H N N 30 5FC "H4'" H N N 31 5FC "H1'" H N N 32 5FC "H3'" H N N 33 5FC "HO3'" H N N 34 5FC H5A H N N 35 5FC HOP3 H N N 36 DA OP3 O N N 37 DA P P N N 38 DA OP1 O N N 39 DA OP2 O N N 40 DA "O5'" O N N 41 DA "C5'" C N N 42 DA "C4'" C N R 43 DA "O4'" O N N 44 DA "C3'" C N S 45 DA "O3'" O N N 46 DA "C2'" C N N 47 DA "C1'" C N R 48 DA N9 N Y N 49 DA C8 C Y N 50 DA N7 N Y N 51 DA C5 C Y N 52 DA C6 C Y N 53 DA N6 N N N 54 DA N1 N Y N 55 DA C2 C Y N 56 DA N3 N Y N 57 DA C4 C Y N 58 DA HOP3 H N N 59 DA HOP2 H N N 60 DA "H5'" H N N 61 DA "H5''" H N N 62 DA "H4'" H N N 63 DA "H3'" H N N 64 DA "HO3'" H N N 65 DA "H2'" H N N 66 DA "H2''" H N N 67 DA "H1'" H N N 68 DA H8 H N N 69 DA H61 H N N 70 DA H62 H N N 71 DA H2 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 DG OP3 O N N 107 DG P P N N 108 DG OP1 O N N 109 DG OP2 O N N 110 DG "O5'" O N N 111 DG "C5'" C N N 112 DG "C4'" C N R 113 DG "O4'" O N N 114 DG "C3'" C N S 115 DG "O3'" O N N 116 DG "C2'" C N N 117 DG "C1'" C N R 118 DG N9 N Y N 119 DG C8 C Y N 120 DG N7 N Y N 121 DG C5 C Y N 122 DG C6 C N N 123 DG O6 O N N 124 DG N1 N N N 125 DG C2 C N N 126 DG N2 N N N 127 DG N3 N N N 128 DG C4 C Y N 129 DG HOP3 H N N 130 DG HOP2 H N N 131 DG "H5'" H N N 132 DG "H5''" H N N 133 DG "H4'" H N N 134 DG "H3'" H N N 135 DG "HO3'" H N N 136 DG "H2'" H N N 137 DG "H2''" H N N 138 DG "H1'" H N N 139 DG H8 H N N 140 DG H1 H N N 141 DG H21 H N N 142 DG H22 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 # 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 5FC P OP2 sing N N 1 5FC P OP1 doub N N 2 5FC P "O5'" sing N N 3 5FC P OP3 sing N N 4 5FC OP2 HOP2 sing N N 5 5FC "O5'" "C5'" sing N N 6 5FC N1 C6 sing N N 7 5FC N1 C2 sing N N 8 5FC N1 "C1'" sing N N 9 5FC C6 C5 doub N N 10 5FC C6 H6 sing N N 11 5FC C2 O2 doub N N 12 5FC C2 N3 sing N N 13 5FC N3 C4 doub N N 14 5FC C4 N4 sing N N 15 5FC C4 C5 sing N N 16 5FC N4 HN41 sing N N 17 5FC N4 HN42 sing N N 18 5FC C5 C5A sing N N 19 5FC "C2'" "C1'" sing N N 20 5FC "C2'" "C3'" sing N N 21 5FC "C2'" "H2'" sing N N 22 5FC "C2'" "H2''" sing N N 23 5FC "C5'" "C4'" sing N N 24 5FC "C5'" "H5'" sing N N 25 5FC "C5'" "H5''" sing N N 26 5FC "C4'" "O4'" sing N N 27 5FC "C4'" "C3'" sing N N 28 5FC "C4'" "H4'" sing N N 29 5FC "O4'" "C1'" sing N N 30 5FC "C1'" "H1'" sing N N 31 5FC "C3'" "O3'" sing N N 32 5FC "C3'" "H3'" sing N N 33 5FC "O3'" "HO3'" sing N N 34 5FC C5A O5A doub N N 35 5FC C5A H5A sing N N 36 5FC OP3 HOP3 sing N N 37 DA OP3 P sing N N 38 DA OP3 HOP3 sing N N 39 DA P OP1 doub N N 40 DA P OP2 sing N N 41 DA P "O5'" sing N N 42 DA OP2 HOP2 sing N N 43 DA "O5'" "C5'" sing N N 44 DA "C5'" "C4'" sing N N 45 DA "C5'" "H5'" sing N N 46 DA "C5'" "H5''" sing N N 47 DA "C4'" "O4'" sing N N 48 DA "C4'" "C3'" sing N N 49 DA "C4'" "H4'" sing N N 50 DA "O4'" "C1'" sing N N 51 DA "C3'" "O3'" sing N N 52 DA "C3'" "C2'" sing N N 53 DA "C3'" "H3'" sing N N 54 DA "O3'" "HO3'" sing N N 55 DA "C2'" "C1'" sing N N 56 DA "C2'" "H2'" sing N N 57 DA "C2'" "H2''" sing N N 58 DA "C1'" N9 sing N N 59 DA "C1'" "H1'" sing N N 60 DA N9 C8 sing Y N 61 DA N9 C4 sing Y N 62 DA C8 N7 doub Y N 63 DA C8 H8 sing N N 64 DA N7 C5 sing Y N 65 DA C5 C6 sing Y N 66 DA C5 C4 doub Y N 67 DA C6 N6 sing N N 68 DA C6 N1 doub Y N 69 DA N6 H61 sing N N 70 DA N6 H62 sing N N 71 DA N1 C2 sing Y N 72 DA C2 N3 doub Y N 73 DA C2 H2 sing N N 74 DA N3 C4 sing Y N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 DG OP3 P sing N N 111 DG OP3 HOP3 sing N N 112 DG P OP1 doub N N 113 DG P OP2 sing N N 114 DG P "O5'" sing N N 115 DG OP2 HOP2 sing N N 116 DG "O5'" "C5'" sing N N 117 DG "C5'" "C4'" sing N N 118 DG "C5'" "H5'" sing N N 119 DG "C5'" "H5''" sing N N 120 DG "C4'" "O4'" sing N N 121 DG "C4'" "C3'" sing N N 122 DG "C4'" "H4'" sing N N 123 DG "O4'" "C1'" sing N N 124 DG "C3'" "O3'" sing N N 125 DG "C3'" "C2'" sing N N 126 DG "C3'" "H3'" sing N N 127 DG "O3'" "HO3'" sing N N 128 DG "C2'" "C1'" sing N N 129 DG "C2'" "H2'" sing N N 130 DG "C2'" "H2''" sing N N 131 DG "C1'" N9 sing N N 132 DG "C1'" "H1'" sing N N 133 DG N9 C8 sing Y N 134 DG N9 C4 sing Y N 135 DG C8 N7 doub Y N 136 DG C8 H8 sing N N 137 DG N7 C5 sing Y N 138 DG C5 C6 sing N N 139 DG C5 C4 doub Y N 140 DG C6 O6 doub N N 141 DG C6 N1 sing N N 142 DG N1 C2 sing N N 143 DG N1 H1 sing N N 144 DG C2 N2 sing N N 145 DG C2 N3 doub N N 146 DG N2 H21 sing N N 147 DG N2 H22 sing N N 148 DG N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4QKK 'double helix' 4QKK 'a-form double helix' # 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 12 8_665 0.038 -0.034 0.359 -27.504 9.561 1.771 1 A_DC1:DG12_A A 1 ? A 12 ? 19 1 1 A DT 2 1_555 A DA 11 8_665 -0.118 -0.184 0.076 12.127 11.690 -1.367 2 A_DT2:DA11_A A 2 ? A 11 ? 20 1 1 A DA 3 1_555 A DT 10 8_665 0.071 -0.066 0.132 17.712 -16.393 1.330 3 A_DA3:DT10_A A 3 ? A 10 ? 20 1 1 A 5FC 4 1_555 A DG 9 8_665 0.264 -0.095 -0.203 15.739 -18.267 1.845 4 A_5FC4:DG9_A A 4 ? A 9 ? 19 1 1 A DG 5 1_555 A 5FC 8 8_665 -0.243 -0.091 -0.014 -4.947 -10.426 1.686 5 A_DG5:5FC8_A A 5 ? A 8 ? 19 1 1 A 5FC 6 1_555 A DG 7 8_665 0.105 -0.106 0.021 1.070 -8.892 -0.419 6 A_5FC6:DG7_A A 6 ? A 7 ? 19 1 1 A DG 7 1_555 A 5FC 6 8_665 -0.105 -0.106 0.021 -1.070 -8.892 -0.419 7 A_DG7:5FC6_A A 7 ? A 6 ? 19 1 1 A 5FC 8 1_555 A DG 5 8_665 0.243 -0.091 -0.014 4.947 -10.427 1.686 8 A_5FC8:DG5_A A 8 ? A 5 ? 19 1 1 A DG 9 1_555 A 5FC 4 8_665 -0.264 -0.095 -0.203 -15.739 -18.267 1.845 9 A_DG9:5FC4_A A 9 ? A 4 ? 19 1 1 A DT 10 1_555 A DA 3 8_665 -0.071 -0.066 0.132 -17.712 -16.393 1.330 10 A_DT10:DA3_A A 10 ? A 3 ? 20 1 1 A DA 11 1_555 A DT 2 8_665 0.118 -0.184 0.076 -12.127 11.690 -1.367 11 A_DA11:DT2_A A 11 ? A 2 ? 20 1 1 A DG 12 1_555 A DC 1 8_665 -0.038 -0.034 0.359 27.504 9.561 1.771 12 A_DG12:DC1_A A 12 ? 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 12 8_665 A DT 2 1_555 A DA 11 8_665 -0.848 1.230 2.740 1.118 13.210 10.109 -4.791 3.693 2.583 52.643 -4.454 16.658 1 AA_DC1DT2:DA11DG12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A DT 2 1_555 A DA 11 8_665 A DA 3 1_555 A DT 10 8_665 -0.181 -0.757 3.216 -3.401 10.031 25.739 -3.856 -0.396 2.735 21.400 7.255 27.799 2 AA_DT2DA3:DT10DA11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A DA 3 1_555 A DT 10 8_665 A 5FC 4 1_555 A DG 9 8_665 0.279 -1.343 3.322 1.107 5.157 36.779 -2.790 -0.291 3.118 8.122 -1.743 37.143 3 AA_DA35FC4:DG9DT10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A 5FC 4 1_555 A DG 9 8_665 A DG 5 1_555 A 5FC 8 8_665 -0.508 -2.055 3.695 -4.745 12.390 26.576 -6.656 -0.020 2.556 25.064 9.598 29.651 4 AA_5FC4DG5:5FC8DG9_AA A 4 ? A 9 ? A 5 ? A 8 ? 1 A DG 5 1_555 A 5FC 8 8_665 A 5FC 6 1_555 A DG 7 8_665 -0.674 -1.479 3.134 -2.103 3.749 36.275 -2.848 0.803 3.005 5.996 3.363 36.520 5 AA_DG55FC6:DG75FC8_AA A 5 ? A 8 ? A 6 ? A 7 ? 1 A 5FC 6 1_555 A DG 7 8_665 A DG 7 1_555 A 5FC 6 8_665 0.000 -1.532 3.268 0.000 16.149 26.184 -5.670 0.000 2.005 32.059 0.000 30.689 6 AA_5FC6DG7:5FC6DG7_AA A 6 ? A 7 ? A 7 ? A 6 ? 1 A DG 7 1_555 A 5FC 6 8_665 A 5FC 8 1_555 A DG 5 8_665 0.674 -1.479 3.134 2.103 3.749 36.275 -2.848 -0.803 3.005 5.996 -3.363 36.520 7 AA_DG75FC8:DG55FC6_AA A 7 ? A 6 ? A 8 ? A 5 ? 1 A 5FC 8 1_555 A DG 5 8_665 A DG 9 1_555 A 5FC 4 8_665 0.508 -2.055 3.695 4.745 12.390 26.576 -6.656 0.020 2.556 25.064 -9.598 29.650 8 AA_5FC8DG9:5FC4DG5_AA A 8 ? A 5 ? A 9 ? A 4 ? 1 A DG 9 1_555 A 5FC 4 8_665 A DT 10 1_555 A DA 3 8_665 -0.279 -1.343 3.322 -1.107 5.157 36.779 -2.790 0.291 3.118 8.122 1.743 37.143 9 AA_DG9DT10:DA35FC4_AA A 9 ? A 4 ? A 10 ? A 3 ? 1 A DT 10 1_555 A DA 3 8_665 A DA 11 1_555 A DT 2 8_665 0.181 -0.757 3.216 3.401 10.031 25.739 -3.856 0.396 2.735 21.400 -7.255 27.799 10 AA_DT10DA11:DT2DA3_AA A 10 ? A 3 ? A 11 ? A 2 ? 1 A DA 11 1_555 A DT 2 8_665 A DG 12 1_555 A DC 1 8_665 0.848 1.230 2.740 -1.118 13.210 10.109 -4.791 -3.693 2.583 52.643 4.454 16.658 11 AA_DA11DG12:DC1DT2_AA A 11 ? A 2 ? A 12 ? A 1 ? # _atom_sites.entry_id 4QKK _atom_sites.fract_transf_matrix[1][1] 0.022526 _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] 0.022526 _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] 0.021620 _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 H N O P # loop_