data_2KV6 # _entry.id 2KV6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2KV6 RCSB RCSB101612 WWPDB D_1000101612 # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KV6 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-03-08 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Huang, H.' 1 'Kozekov, I.D.' 2 'Kozekova, A.' 3 'Rizzo, C.J.' 4 'McCullough, A.' 5 'LLoyd, R.S.' 6 'Stone, M.P.' 7 # _citation.id primary _citation.title ;Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage . ; _citation.journal_abbrev Biochemistry _citation.journal_volume 49 _citation.page_first 6155 _citation.page_last 6164 _citation.year 2010 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20604523 _citation.pdbx_database_id_DOI 10.1021/bi100364f # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Huang, H.' 1 primary 'Kozekov, I.D.' 2 primary 'Kozekova, A.' 3 primary 'Rizzo, C.J.' 4 primary 'McCullough, A.K.' 5 primary 'Lloyd, R.S.' 6 primary 'Stone, M.P.' 7 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'" 3705.472 1 ? ? ? ? 2 polymer syn "5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'" 3663.392 1 ? ? ? ? 3 polymer syn 'KWKK Tetrapeptide' 591.764 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DG)(DC)(DT)(DA)(DG)(DC)(0AD)(DA)(DG)(DT)(DC)(DC)' GCTAGCGAGTCC A ? 2 polydeoxyribonucleotide no no '(DG)(DG)(DA)(DC)(DT)(DC)(DG)(DC)(DT)(DA)(DG)(DC)' GGACTCGCTAGC B ? 3 'polypeptide(L)' no no KWKK KWKK C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DT n 1 4 DA n 1 5 DG n 1 6 DC n 1 7 0AD n 1 8 DA n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC n 2 1 DG n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DT n 2 6 DC n 2 7 DG n 2 8 DC n 2 9 DT n 2 10 DA n 2 11 DG n 2 12 DC n 3 1 LYS n 3 2 TRP n 3 3 LYS n 3 4 LYS n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2KV6 2KV6 1 ? GCTAGCGAGTCC ? 2 PDB 2KV6 2KV6 2 ? GGACTCGCTAGC ? 3 PDB 2KV6 2KV6 3 ? KWKK ? # 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 2KV6 A 1 ? 12 ? 2KV6 1 ? 12 ? 1 12 2 2 2KV6 B 1 ? 12 ? 2KV6 13 ? 24 ? 13 24 3 3 2KV6 C 1 ? 4 ? 2KV6 26 ? 29 ? 26 29 # 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 0AD 'DNA linking' n ;2'-deoxy-N-propylguanosine 5'-(dihydrogen phosphate) ; ? 'C13 H20 N5 O7 P' 389.301 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 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H COSY' 1 3 1 '2D 1H-1H TOCSY' 1 4 1 '2D DQF-COSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 100 _pdbx_nmr_exptl_sample_conditions.pH 5.3 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents ;0.8 mM DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-1, 0.8 mM DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')-2, 0.8 mM entity_3-3, 100% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model Avance _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KV6 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KV6 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KV6 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_software.authors 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name AMBER _pdbx_nmr_software.version 7.0 _pdbx_nmr_software.ordinal 1 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KV6 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KV6 _struct.title 'Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether' _struct.pdbx_descriptor 'PROTEIN/DNA Complex' _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KV6 _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN/DNA' _struct_keywords.text 'DNA-peptide conjugate, trimethylene, acrolein-dG adduct, DNA-peptide complex, DNA BINDING PROTEIN-DNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _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 covale1 covale ? ? A 0AD 7 C6A ? ? ? 1_555 C LYS 1 N ? ? A 0AD 7 C LYS 26 1_555 ? ? ? ? ? ? ? 1.487 ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A 0AD 7 N1 ? ? ? 1_555 B DC 6 N3 ? ? A 0AD 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A 0AD 7 N2 ? ? ? 1_555 B DC 6 O2 ? ? A 0AD 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A 0AD 7 O6 ? ? ? 1_555 B DC 6 N4 ? ? A 0AD 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog32 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2KV6 _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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_ _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 DG 1 1 1 DG DG A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 0AD 7 7 7 0AD 0AD A . n A 1 8 DA 8 8 8 DA DA 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 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC A . n B 2 1 DG 1 13 13 DG DG B . n B 2 2 DG 2 14 14 DG DG B . n B 2 3 DA 3 15 15 DA DA B . n B 2 4 DC 4 16 16 DC DC B . n B 2 5 DT 5 17 17 DT DT B . n B 2 6 DC 6 18 18 DC DC B . n B 2 7 DG 7 19 19 DG DG B . n B 2 8 DC 8 20 20 DC DC B . n B 2 9 DT 9 21 21 DT DT B . n B 2 10 DA 10 22 22 DA DA B . n B 2 11 DG 11 23 23 DG DG B . n B 2 12 DC 12 24 24 DC DC B . n C 3 1 LYS 1 26 26 LYS LYS C . n C 3 2 TRP 2 27 27 TRP TRP C . n C 3 3 LYS 3 28 28 LYS LYS C . n C 3 4 LYS 4 29 29 LYS LYS C . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 0AD _pdbx_struct_mod_residue.label_seq_id 7 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 0AD _pdbx_struct_mod_residue.auth_seq_id 7 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DG _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 # 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 2010-07-21 2 'Structure model' 1 1 2011-07-13 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-1 ; 0.8 ? mM ? 1 ;DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')-2 ; 0.8 ? mM ? 1 entity_3-3 0.8 ? mM ? 1 # 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 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 116.98 121.90 -4.92 0.70 N 2 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.30 108.30 2.00 0.30 N 3 1 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.65 117.00 -3.35 0.50 N 4 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 121.38 117.70 3.68 0.50 N 5 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 113.66 118.60 -4.94 0.60 N 6 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.15 108.30 1.85 0.30 N 7 1 N3 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 116.68 121.90 -5.22 0.70 N 8 1 C4 A DA 8 ? ? C5 A DA 8 ? ? C6 A DA 8 ? ? 113.32 117.00 -3.68 0.50 N 9 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 121.11 117.70 3.41 0.50 N 10 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 112.86 118.60 -5.74 0.60 N 11 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 111.16 108.30 2.86 0.30 N 12 1 N3 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 117.06 121.90 -4.84 0.70 N 13 1 N3 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 116.89 121.90 -5.01 0.70 N 14 1 C4 B DA 15 ? ? C5 B DA 15 ? ? C6 B DA 15 ? ? 113.95 117.00 -3.05 0.50 N 15 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 121.42 117.70 3.72 0.50 N 16 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 114.07 118.60 -4.53 0.60 N 17 1 "O4'" B DC 16 ? ? "C1'" B DC 16 ? ? N1 B DC 16 ? ? 111.72 108.30 3.42 0.30 N 18 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 116.95 121.90 -4.95 0.70 N 19 1 C6 B DT 17 ? ? C5 B DT 17 ? ? C7 B DT 17 ? ? 119.28 122.90 -3.62 0.60 N 20 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 110.99 108.30 2.69 0.30 N 21 1 N3 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 116.99 121.90 -4.91 0.70 N 22 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 110.34 108.30 2.04 0.30 N 23 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 116.73 121.90 -5.17 0.70 N 24 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 110.73 108.30 2.43 0.30 N 25 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 119.25 122.90 -3.65 0.60 N 26 1 C4 B DA 22 ? ? C5 B DA 22 ? ? C6 B DA 22 ? ? 113.59 117.00 -3.41 0.50 N 27 1 C5 B DA 22 ? ? C6 B DA 22 ? ? N1 B DA 22 ? ? 121.21 117.70 3.51 0.50 N 28 1 N1 B DA 22 ? ? C6 B DA 22 ? ? N6 B DA 22 ? ? 113.77 118.60 -4.83 0.60 N 29 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 110.52 108.30 2.22 0.30 N 30 1 N1 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 122.51 118.90 3.61 0.60 N 31 1 N3 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 116.73 121.90 -5.17 0.70 N # _ndb_struct_conf_na.entry_id 2KV6 _ndb_struct_conf_na.feature 'b-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 DG 1 1_555 B DC 12 1_555 -0.545 -0.139 -0.028 -5.977 -6.375 -0.586 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DC 2 1_555 B DG 11 1_555 0.422 -0.138 0.147 -3.006 -7.658 -1.299 2 A_DC2:DG23_B A 2 ? B 23 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 0.013 -0.028 -0.044 3.885 -13.741 -0.399 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 0.051 -0.006 -0.112 -6.513 -15.235 -1.549 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DG 5 1_555 B DC 8 1_555 -0.529 -0.147 0.065 -4.326 -6.593 -0.278 5 A_DG5:DC20_B A 5 ? B 20 ? 19 1 1 A DC 6 1_555 B DG 7 1_555 0.370 -0.106 0.068 -2.352 2.457 -1.269 6 A_DC6:DG19_B A 6 ? B 19 ? 19 1 1 A 0AD 7 1_555 B DC 6 1_555 0.090 -0.023 -0.003 7.339 -8.173 0.173 7 A_0AD7:DC18_B A 7 ? B 18 ? 19 1 1 A DA 8 1_555 B DT 5 1_555 0.274 -0.012 -0.182 7.083 -16.715 3.991 8 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.615 -0.183 -0.056 -10.472 -19.591 0.841 9 A_DG9:DC16_B A 9 ? B 16 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.139 0.035 0.038 -18.534 -14.037 -3.446 10 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.450 -0.157 -0.025 -9.058 -7.207 -0.563 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DC 12 1_555 B DG 1 1_555 0.434 -0.096 -0.125 -3.594 -3.205 0.165 12 A_DC12:DG13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B DC 12 1_555 A DC 2 1_555 B DG 11 1_555 -0.810 -0.555 3.283 -2.159 1.475 35.118 -1.139 1.016 3.300 2.440 3.572 35.212 1 AA_DG1DC2:DG23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DC 2 1_555 B DG 11 1_555 A DT 3 1_555 B DA 10 1_555 0.545 -0.195 3.108 2.024 5.722 30.802 -1.383 -0.646 3.052 10.643 -3.765 31.380 2 AA_DC2DT3:DA22DG23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DT 3 1_555 B DA 10 1_555 A DA 4 1_555 B DT 9 1_555 -0.085 -1.212 3.410 -0.798 19.090 29.759 -4.681 0.028 2.253 33.212 1.388 35.248 3 AA_DT3DA4:DT21DA22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DG 5 1_555 B DC 8 1_555 0.015 -1.316 3.231 -2.165 5.355 27.403 -3.924 -0.518 2.916 11.147 4.507 27.994 4 AA_DA4DG5:DC20DT21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B DC 8 1_555 A DC 6 1_555 B DG 7 1_555 -0.579 -0.830 3.362 -0.471 3.469 33.885 -1.978 0.913 3.271 5.932 0.805 34.060 5 AA_DG5DC6:DG19DC20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DC 6 1_555 B DG 7 1_555 A 0AD 7 1_555 B DC 6 1_555 0.696 0.064 3.216 2.026 15.326 30.819 -2.282 -0.861 2.958 26.826 -3.546 34.395 6 AA_DC60AD7:DC18DG19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A 0AD 7 1_555 B DC 6 1_555 A DA 8 1_555 B DT 5 1_555 -0.712 0.144 3.322 0.106 6.388 36.159 -0.661 1.145 3.296 10.194 -0.169 36.700 7 AA_0AD7DA8:DT17DC18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DA 8 1_555 B DT 5 1_555 A DG 9 1_555 B DC 4 1_555 0.048 -1.305 3.696 -5.387 9.032 29.708 -4.217 -1.169 3.119 16.960 10.116 31.475 8 AA_DA8DG9:DC16DT17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DG 9 1_555 B DC 4 1_555 A DT 10 1_555 B DA 3 1_555 -1.018 -1.130 3.491 0.102 -0.292 35.899 -1.788 1.667 3.497 -0.474 -0.165 35.900 9 AA_DG9DT10:DA15DC16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DT 10 1_555 B DA 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.034 0.373 3.138 -1.292 5.262 38.865 -0.053 -0.098 3.159 7.861 1.931 39.226 10 AA_DT10DC11:DG14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DC 12 1_555 B DG 1 1_555 0.030 -0.064 3.230 2.390 3.354 28.268 -0.882 0.475 3.192 6.822 -4.861 28.560 11 AA_DC11DC12:DG13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? #