data_2KDQ # _entry.id 2KDQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2KDQ pdb_00002kdq 10.2210/pdb2kdq/pdb RCSB RCSB100993 ? ? WWPDB D_1000100993 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2a9x PDB 'BIV TAR and cyclic peptide mimicking BIV Tat' unspecified 2ns4 PDB 'Unbound L-22 solution structure' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KDQ _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2009-01-14 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Davidson, A.' 1 'Leeper, T.C.' 2 'Varani, G.' 3 # _citation.id primary _citation.title 'Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 106 _citation.page_first 11931 _citation.page_last 11936 _citation.year 2009 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19584251 _citation.pdbx_database_id_DOI 10.1073/pnas.0900629106 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Davidson, A.' 1 ? primary 'Leeper, T.C.' 2 ? primary 'Athanassiou, Z.' 3 ? primary 'Patora-Komisarska, K.' 4 ? primary 'Karn, J.' 5 ? primary 'Robinson, J.A.' 6 ? primary 'Varani, G.' 7 ? # _cell.entry_id 2KDQ _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2KDQ _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 'L-22 CYCLIC PEPTIDE' 1768.189 1 ? ? ? ? 2 polymer syn 'HIV-1 TAR RNA' 9307.555 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 'polypeptide(L)' no yes 'RVRTRKGRRIRI(DPR)P' RVRTRKGRRIRIPP A ? 2 polyribonucleotide no no GGCAGAUCUGAGCCUGGGAGCUCUCUGCC GGCAGAUCUGAGCCUGGGAGCUCUCUGCC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ARG n 1 2 VAL n 1 3 ARG n 1 4 THR n 1 5 ARG n 1 6 LYS n 1 7 GLY n 1 8 ARG n 1 9 ARG n 1 10 ILE n 1 11 ARG n 1 12 ILE n 1 13 DPR n 1 14 PRO n 2 1 G n 2 2 G n 2 3 C n 2 4 A n 2 5 G n 2 6 A n 2 7 U n 2 8 C n 2 9 U n 2 10 G n 2 11 A n 2 12 G n 2 13 C n 2 14 C n 2 15 U n 2 16 G n 2 17 G n 2 18 G n 2 19 A n 2 20 G n 2 21 C n 2 22 U n 2 23 C n 2 24 U n 2 25 C n 2 26 U n 2 27 G n 2 28 C n 2 29 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'THE L-22 PEPTIDE WAS SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC' 2 1 sample ? ? ? ? ? ;RNA WAS TRANSCRIBED IN VITRO FROM DNA OLIGONUCLEOTIDE TEMPLATES WITH T7 RNA POLYMERASE PURIFIED IN HOUSE WITH UNLABELED OR 13C/15N ENRICHED NTPS (ISOTEC) AND PURIFIED BY DENATURING PAGE. ; # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 PDB 2KDQ 2KDQ 1 RVRTRKGRRIRIPP 1 ? 2 PDB 2KDQ 2KDQ 2 GGCAGAUCUGAGCCUGGGAGCUCUCUGCC 1 ? # 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 2KDQ A 1 ? 14 ? 2KDQ 1 ? 14 ? 1 14 2 2 2KDQ B 1 ? 29 ? 2KDQ 17 ? 45 ? 17 45 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DPR 'D-peptide linking' . D-PROLINE ? 'C5 H9 N O2' 115.130 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 3 '3D-13C HMQC NOESY, 3D HCCH TOCSY, IPAP-HSQC' 2 2 4 '15N HSQC' 1 3 1 '2D noesy' 2 4 2 '2D watergate NOESY' 1 5 3 'F1fF2f-type noesy, F1fF2f-type tocsy, 2D HCCH-COSY' 1 6 5 '2D 1H-1H NOESY' 2 7 4 'F1fF2f-type watergate noesy' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 '10 mM potassium phosphate' 6.6 ambient ? 298 K 2 '10 mM potassium phosphate' 6.6 ambient ? 277 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1.0mM HIV-1 TAR RNA-1, 1.0mM L-22 CYCLIC PEPTIDE-2, 100% D2O' 1 '100% D2O' '1.0mM HIV-1 TAR RNA-3, 1.0mM L-22 CYCLIC PEPTIDE-4, 90 % H2O, 10% D2O' 2 '90% H2O/10% D2O' '1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-5, 1.0mM L-22 CYCLIC PEPTIDE-6, 100% D2O' 3 '100% D2O' '1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-7, 1.0mM L-22 CYCLIC PEPTIDE-8, 90 % H2O, 10% D2O' 4 '90% H2O/10% D2O' '1.0mM [U-2H] HIV-1 TAR RNA-9, 1.0mM L-22 CYCLIC PEPTIDE-10, 100% D2O' 5 '100% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker DRX 1 'Bruker DRX' 600 Bruker DMX 2 'Bruker DMX' 800 Varian INOVA 3 'Varian Inova' 600 Bruker AVIII 4 'Bruker AVIII' # _pdbx_nmr_refine.entry_id 2KDQ _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;Structures of the HIV-1 TAR RNA/L-22 complex were calculated with Xplor-NIH. Backbone dihedral angle restraints for the peptide were estimated using chemical shift data and TALOS. Structures were originally calculated without RDCs to test for convergence and adherence to the NOE data. RDC restraints were then applied as susceptibility anisotropy restraints with a harmonic potential well. ; _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 'Lowest energy, least restraint violations' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KDQ _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.representative_conformer 7 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KDQ _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore' 'structure solution' 'X-PLOR NIH' 2.16.0 1 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe . 2 'Bruker Biospin' collection TopSpin . 3 'Cornilescu, Delaglio and Bax' 'data analysis' TALOS . 4 Goddard 'peak picking' Sparky . 5 'C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore' refinement 'X-PLOR NIH' 2.16.0 6 # _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 2KDQ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KDQ _struct.title 'Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein' _struct.pdbx_model_details 'lowest energy, model 7' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KDQ _struct_keywords.pdbx_keywords 'RNA binding protein/RNA' _struct_keywords.text ;PEPTIDOMIMETICS, PEPTIDE STRUCTURE, RNA RECOGNITION, IMMUNODEFICIENCY VIRUS, TAR RNA, mimic of RNA binding protein, RNA binding protein-RNA 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 ? # _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 covale1 covale both ? A ARG 1 N ? ? ? 1_555 A PRO 14 C ? ? A ARG 1 A PRO 14 1_555 ? ? ? ? ? ? ? 1.313 ? ? covale2 covale both ? A ILE 12 C ? ? ? 1_555 A DPR 13 N ? ? A ILE 12 A DPR 13 1_555 ? ? ? ? ? ? ? 1.309 ? ? covale3 covale both ? A DPR 13 C ? ? ? 1_555 A PRO 14 N ? ? A DPR 13 A PRO 14 1_555 ? ? ? ? ? ? ? 1.306 ? ? hydrog1 hydrog ? ? B G 1 N1 ? ? ? 1_555 B C 29 N3 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B G 1 N2 ? ? ? 1_555 B C 29 O2 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B G 1 O6 ? ? ? 1_555 B C 29 N4 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B G 2 N1 ? ? ? 1_555 B C 28 N3 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B G 2 N2 ? ? ? 1_555 B C 28 O2 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B G 2 O6 ? ? ? 1_555 B C 28 N4 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B C 3 N3 ? ? ? 1_555 B G 27 N1 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B C 3 N4 ? ? ? 1_555 B G 27 O6 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B C 3 O2 ? ? ? 1_555 B G 27 N2 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B A 4 N1 ? ? ? 1_555 B U 26 N3 ? ? B A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B A 4 N6 ? ? ? 1_555 B U 26 O4 ? ? B A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B G 5 N1 ? ? ? 1_555 B C 25 N3 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B G 5 N2 ? ? ? 1_555 B C 25 O2 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B G 5 O6 ? ? ? 1_555 B C 25 N4 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B A 6 N1 ? ? ? 1_555 B U 24 N3 ? ? B A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B A 6 N6 ? ? ? 1_555 B U 24 O4 ? ? B A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B U 7 N3 ? ? ? 1_555 B A 11 N7 ? ? B U 23 B A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? B U 7 O4 ? ? ? 1_555 B A 11 N6 ? ? B U 23 B A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? B G 10 N1 ? ? ? 1_555 B C 23 N3 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B G 10 N2 ? ? ? 1_555 B C 23 O2 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B G 10 O6 ? ? ? 1_555 B C 23 N4 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B A 11 N1 ? ? ? 1_555 B U 22 N3 ? ? B A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B A 11 N6 ? ? ? 1_555 B U 22 O4 ? ? B A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B G 12 N1 ? ? ? 1_555 B C 21 N3 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B G 12 N2 ? ? ? 1_555 B C 21 O2 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B G 12 O6 ? ? ? 1_555 B C 21 N4 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B G 12 O6 ? ? ? 1_555 B U 22 N3 ? ? B G 28 B U 38 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog28 hydrog ? ? B C 13 N3 ? ? ? 1_555 B G 16 N1 ? ? B C 29 B G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B C 13 N4 ? ? ? 1_555 B G 16 O6 ? ? B C 29 B G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 13 O2 ? ? ? 1_555 B G 16 N2 ? ? B C 29 B G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 13 N3 ? ? ? 1_555 B G 20 N1 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 13 N4 ? ? ? 1_555 B G 20 O6 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 13 O2 ? ? ? 1_555 B G 20 N2 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 VAL A 2 ? ARG A 5 ? VAL A 2 ARG A 5 A 2 ARG A 8 ? ARG A 11 ? ARG A 8 ARG A 11 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id ARG _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 5 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id ARG _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 5 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id ARG _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 8 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id ARG _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 8 # _atom_sites.entry_id 2KDQ _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 ARG 1 1 1 ARG ARG A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 ARG 3 3 3 ARG ARG A . n A 1 4 THR 4 4 4 THR THR A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 ARG 9 9 9 ARG ARG A . n A 1 10 ILE 10 10 10 ILE ILE A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 DPR 13 13 13 DPR DPR A . n A 1 14 PRO 14 14 14 PRO PRO A . n B 2 1 G 1 17 17 G G B . n B 2 2 G 2 18 18 G G B . n B 2 3 C 3 19 19 C C B . n B 2 4 A 4 20 20 A A B . n B 2 5 G 5 21 21 G G B . n B 2 6 A 6 22 22 A A B . n B 2 7 U 7 23 23 U U B . n B 2 8 C 8 24 24 C C B . n B 2 9 U 9 25 25 U U B . n B 2 10 G 10 26 26 G G B . n B 2 11 A 11 27 27 A A B . n B 2 12 G 12 28 28 G G B . n B 2 13 C 13 29 29 C C B . n B 2 14 C 14 30 30 C C B . n B 2 15 U 15 31 31 U U B . n B 2 16 G 16 32 32 G G B . n B 2 17 G 17 33 33 G G B . n B 2 18 G 18 34 34 G G B . n B 2 19 A 19 35 35 A A B . n B 2 20 G 20 36 36 G G B . n B 2 21 C 21 37 37 C C B . n B 2 22 U 22 38 38 U U B . n B 2 23 C 23 39 39 C C B . n B 2 24 U 24 40 40 U U B . n B 2 25 C 25 41 41 C C B . n B 2 26 U 26 42 42 U U B . n B 2 27 G 27 43 43 G G B . n B 2 28 C 28 44 44 C C B . n B 2 29 C 29 45 45 C C B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2009-06-23 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_struct_assembly 4 3 'Structure model' pdbx_struct_oper_list 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_ref_seq # 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' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_struct_conn.pdbx_dist_value' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 3 'Structure model' '_struct_ref_seq.db_align_beg' 17 3 'Structure model' '_struct_ref_seq.db_align_end' # 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 entity_3-1 1.0 ? mM ? 1 entity_6-2 1.0 ? mM ? 1 entity_3-3 1.0 ? mM ? 2 entity_6-4 1.0 ? mM ? 2 entity_3-5 1.0 ? mM '[U-98% 13C; U-98% 15N]' 3 entity_6-6 1.0 ? mM ? 3 entity_3-7 1.0 ? mM '[U-98% 13C; U-98% 15N]' 4 entity_6-8 1.0 ? mM ? 4 entity_3-9 1.0 ? mM '[U-2H]' 5 entity_6-10 1.0 ? mM ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "H3'" B C 24 ? ? "H5'" B U 25 ? ? 1.25 2 1 "H4'" B G 32 ? ? "H5'" B G 33 ? ? 1.29 3 1 "H2'" B A 27 ? ? H8 B G 28 ? ? 1.30 4 1 HH21 A ARG 1 ? ? HH12 A ARG 3 ? ? 1.34 5 1 "HO2'" B G 34 ? ? OP1 B A 35 ? ? 1.42 6 1 OP1 B C 24 ? ? "HO2'" B U 25 ? ? 1.47 7 1 O A ARG 5 ? ? H A ARG 8 ? ? 1.50 8 1 "HO2'" B G 18 ? ? "O4'" B C 19 ? ? 1.52 9 1 N1 B A 20 ? ? H3 B U 42 ? ? 1.53 10 1 O4 B U 23 ? ? H62 B A 27 ? ? 1.55 11 1 OP2 B U 31 ? ? "HO2'" B G 32 ? ? 1.56 12 1 "H4'" B G 33 ? ? "O5'" B G 34 ? ? 1.56 13 1 O A ARG 9 ? ? "H2'" B G 34 ? ? 1.58 14 1 H3 B U 23 ? ? N7 B A 27 ? ? 1.59 15 2 "H1'" B G 32 ? ? H1 B G 34 ? ? 1.14 16 2 HH22 A ARG 9 ? ? "H3'" B G 34 ? ? 1.17 17 2 HH22 A ARG 5 ? ? "H3'" B A 27 ? ? 1.22 18 2 HH22 A ARG 3 ? ? H8 B A 22 ? ? 1.23 19 2 "H5'" B C 24 ? ? "H5'" B U 25 ? ? 1.24 20 2 "O2'" B G 28 ? ? "H5'" B C 29 ? ? 1.53 21 2 O4 B U 23 ? ? H62 B A 27 ? ? 1.53 22 2 "HO2'" B U 25 ? ? OP1 B G 26 ? ? 1.56 23 3 HH21 A ARG 9 ? ? "H2'" B G 33 ? ? 1.14 24 3 "H2'" B G 36 ? ? H6 B C 37 ? ? 1.32 25 3 "HO2'" B C 39 ? ? "O4'" B U 40 ? ? 1.44 26 3 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.50 27 3 "HO2'" B G 32 ? ? "O3'" B G 33 ? ? 1.54 28 3 O4 B U 23 ? ? H62 B A 27 ? ? 1.57 29 3 H3 B U 23 ? ? N7 B A 27 ? ? 1.58 30 3 O6 B G 28 ? ? H1 B G 34 ? ? 1.58 31 3 N A ARG 1 ? ? O A PRO 14 ? ? 2.19 32 4 "H5''" B C 24 ? ? "H5'" B U 25 ? ? 1.18 33 4 HH11 A ARG 9 ? ? HH22 A ARG 11 ? ? 1.23 34 4 "H2'" B G 32 ? ? "H4'" B G 34 ? ? 1.29 35 4 HE A ARG 11 ? ? "O3'" B G 34 ? ? 1.40 36 4 O A THR 4 ? ? "H3'" B U 23 ? ? 1.50 37 4 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.50 38 4 "HO2'" B C 39 ? ? "O5'" B U 40 ? ? 1.53 39 4 O4 B U 23 ? ? H62 B A 27 ? ? 1.54 40 4 "H4'" B A 35 ? ? OP1 B G 36 ? ? 1.55 41 4 O A ARG 1 ? ? H A ILE 12 ? ? 1.57 42 4 O A ARG 5 ? ? H A ARG 8 ? ? 1.57 43 4 "O2'" B C 37 ? ? "H5'" B U 38 ? ? 1.58 44 4 NE A ARG 11 ? ? "O3'" B G 34 ? ? 2.16 45 5 HH22 A ARG 3 ? ? H8 B A 22 ? ? 1.11 46 5 "H1'" B G 32 ? ? "H5''" B G 33 ? ? 1.17 47 5 "H2'" B G 36 ? ? H6 B C 37 ? ? 1.27 48 5 "H3'" B G 28 ? ? H42 B C 30 ? ? 1.29 49 5 "H1'" B G 32 ? ? "H3'" B G 33 ? ? 1.32 50 5 HH22 A ARG 9 ? ? "O2'" B G 34 ? ? 1.40 51 5 "O2'" B C 37 ? ? "H5'" B U 38 ? ? 1.51 52 5 O4 B U 23 ? ? H62 B A 27 ? ? 1.54 53 5 "HO2'" B G 33 ? ? OP1 B G 34 ? ? 1.55 54 5 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.57 55 5 HH12 A ARG 9 ? ? "O2'" B G 34 ? ? 1.57 56 5 "O2'" B G 28 ? ? "H5'" B C 29 ? ? 1.58 57 6 HH22 A ARG 8 ? ? "H5''" B G 33 ? ? 1.09 58 6 "H5'" B C 24 ? ? "H2'" B U 25 ? ? 1.18 59 6 HH12 A ARG 11 ? ? "HO2'" B G 34 ? ? 1.19 60 6 "HO2'" B G 32 ? ? "H5'" B G 33 ? ? 1.28 61 6 HE A ARG 9 ? ? "O2'" B G 34 ? ? 1.32 62 6 "H4'" B C 30 ? ? H5 B U 31 ? ? 1.35 63 6 "HO2'" B C 39 ? ? "O4'" B U 40 ? ? 1.41 64 6 HE A ARG 3 ? ? OP2 B U 23 ? ? 1.44 65 6 "O2'" B G 28 ? ? "H5'" B C 29 ? ? 1.52 66 6 H A LYS 6 ? ? OP2 B C 24 ? ? 1.53 67 6 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.54 68 6 "HO2'" B U 38 ? ? "O4'" B C 39 ? ? 1.57 69 6 H3 B U 23 ? ? N7 B A 27 ? ? 1.60 70 7 HH21 A ARG 9 ? ? HH21 A ARG 11 ? ? 1.24 71 7 HH11 A ARG 8 ? ? H A ARG 9 ? ? 1.26 72 7 "HO2'" B G 18 ? ? "O5'" B C 19 ? ? 1.44 73 7 O A ARG 5 ? ? H A ARG 8 ? ? 1.53 74 7 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.54 75 7 O4 B U 23 ? ? H62 B A 27 ? ? 1.54 76 7 "HO2'" B U 38 ? ? "O4'" B C 39 ? ? 1.58 77 8 HH21 A ARG 9 ? ? HH21 A ARG 11 ? ? 1.15 78 8 "H3'" B C 24 ? ? H6 B U 25 ? ? 1.23 79 8 "HO2'" B U 23 ? ? "H4'" B C 24 ? ? 1.32 80 8 HH22 A ARG 1 ? ? N7 B A 22 ? ? 1.48 81 8 O A ARG 5 ? ? H A ARG 8 ? ? 1.50 82 8 O4 B U 23 ? ? H62 B A 27 ? ? 1.51 83 8 "HO2'" B C 39 ? ? "O4'" B U 40 ? ? 1.51 84 8 "O2'" B C 37 ? ? "H5'" B U 38 ? ? 1.52 85 8 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.52 86 8 "O2'" B G 28 ? ? "H5'" B C 29 ? ? 1.56 87 8 HE A ARG 11 ? ? "O2'" B G 34 ? ? 1.59 88 9 HH22 A ARG 3 ? ? H8 B A 22 ? ? 1.24 89 9 HE A ARG 9 ? ? "H5'" B G 34 ? ? 1.27 90 9 O A ARG 5 ? ? H A ARG 8 ? ? 1.42 91 9 "O2'" B A 27 ? ? "H5'" B G 28 ? ? 1.52 92 9 OP2 B C 24 ? ? "H2'" B U 25 ? ? 1.53 93 9 O A ARG 1 ? ? H A ILE 12 ? ? 1.57 94 9 O4 B U 23 ? ? H62 B A 27 ? ? 1.58 95 9 H3 B U 23 ? ? N7 B A 27 ? ? 1.59 96 9 "O2'" B C 37 ? ? "H5'" B U 38 ? ? 1.59 97 9 N1 B A 20 ? ? H3 B U 42 ? ? 1.59 98 10 HH21 A ARG 9 ? ? "H2'" B G 34 ? ? 1.23 99 10 HE A ARG 8 ? ? "H2'" B U 31 ? ? 1.25 100 10 "H1'" B G 32 ? ? "H5''" B G 34 ? ? 1.26 101 10 HH22 A ARG 9 ? ? H8 B G 32 ? ? 1.28 102 10 HE A ARG 3 ? ? H5 B U 23 ? ? 1.29 103 10 H1 B G 21 ? ? H41 B C 41 ? ? 1.32 104 10 O A ARG 5 ? ? H A ARG 8 ? ? 1.41 105 10 O4 B U 23 ? ? H62 B A 27 ? ? 1.52 106 10 "O2'" B G 28 ? ? "H5'" B C 29 ? ? 1.58 107 10 O2 B U 23 ? ? "H2'" B G 26 ? ? 1.59 108 10 N A ARG 1 ? ? O A PRO 14 ? ? 2.15 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 3 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C4'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 34 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 34 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.617 _pdbx_validate_rmsd_bond.bond_target_value 1.527 _pdbx_validate_rmsd_bond.bond_deviation 0.090 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.011 _pdbx_validate_rmsd_bond.linker_flag 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 "C5'" B C 24 ? ? "C4'" B C 24 ? ? "C3'" B C 24 ? ? 106.75 115.20 -8.45 1.40 N 2 3 "C5'" B A 35 ? ? "C4'" B A 35 ? ? "C3'" B A 35 ? ? 104.29 115.20 -10.91 1.40 N 3 5 "C5'" B U 23 ? ? "C4'" B U 23 ? ? "C3'" B U 23 ? ? 106.74 115.20 -8.46 1.40 N 4 6 "C5'" B U 23 ? ? "C4'" B U 23 ? ? "C3'" B U 23 ? ? 106.71 115.20 -8.49 1.40 N 5 6 "C5'" B G 34 ? ? "C4'" B G 34 ? ? "C3'" B G 34 ? ? 106.78 115.20 -8.42 1.40 N 6 10 "C5'" B C 24 ? ? "C4'" B C 24 ? ? "C3'" B C 24 ? ? 106.74 115.20 -8.46 1.40 N 7 10 "C5'" B G 33 ? ? "C4'" B G 33 ? ? "C3'" B G 33 ? ? 106.62 115.20 -8.58 1.40 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 2 DPR A 13 ? ? 58.61 -108.43 2 3 LYS A 6 ? ? 40.88 27.64 3 4 LYS A 6 ? ? 40.54 28.45 4 4 DPR A 13 ? ? 59.49 -108.72 5 5 ARG A 9 ? ? -65.91 93.62 6 6 LYS A 6 ? ? 40.04 29.30 7 7 LYS A 6 ? ? 38.71 29.13 8 8 LYS A 6 ? ? 38.61 43.71 9 9 LYS A 6 ? ? 42.89 28.17 10 9 DPR A 13 ? ? 56.21 -103.56 11 10 LYS A 6 ? ? 45.42 25.71 12 10 DPR A 13 ? ? 48.71 -105.53 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 8 G B 34 ? ? 0.060 'SIDE CHAIN' 2 9 G B 34 ? ? 0.053 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KDQ 'double helix' 2KDQ 'a-form double helix' 2KDQ 'bulge loop' 2KDQ 'internal loop' # 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 B G 1 1_555 B C 29 1_555 -1.355 -0.827 -0.016 -0.847 0.785 -2.191 1 B_G17:C45_B B 17 ? B 45 ? 19 1 1 B G 2 1_555 B C 28 1_555 -1.394 -0.848 0.419 20.864 -13.864 -2.020 2 B_G18:C44_B B 18 ? B 44 ? 19 1 1 B C 3 1_555 B G 27 1_555 -0.587 -0.050 -0.188 8.996 -8.524 3.927 3 B_C19:G43_B B 19 ? B 43 ? 19 1 1 B A 4 1_555 B U 26 1_555 0.098 -0.316 -0.092 1.792 16.070 10.487 4 B_A20:U42_B B 20 ? B 42 ? 20 1 1 B G 5 1_555 B C 25 1_555 -0.363 -0.083 0.018 -6.343 -1.021 3.720 5 B_G21:C41_B B 21 ? B 41 ? 19 1 1 B A 6 1_555 B U 24 1_555 1.233 -0.296 -0.228 3.173 8.850 -7.385 6 B_A22:U40_B B 22 ? B 40 ? 20 1 1 B G 10 1_555 B C 23 1_555 0.674 -0.140 -0.079 -8.439 17.973 6.317 7 B_G26:C39_B B 26 ? B 39 ? 19 1 1 B A 11 1_555 B U 22 1_555 -0.845 -0.611 -0.245 0.475 9.461 -2.452 8 B_A27:U38_B B 27 ? B 38 ? 20 1 1 B G 12 1_555 B C 21 1_555 0.375 -0.224 -0.313 2.466 22.094 -7.370 9 B_G28:C37_B B 28 ? B 37 ? 19 1 1 B C 13 1_555 B G 20 1_555 -0.097 -0.269 0.016 10.355 29.734 9.566 10 B_C29:G36_B B 29 ? B 36 ? 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 B G 1 1_555 B C 29 1_555 B G 2 1_555 B C 28 1_555 0.244 1.120 2.950 -0.881 16.756 30.909 -0.634 -0.537 3.125 28.923 1.520 35.071 1 BB_G17G18:C44C45_BB B 17 ? B 45 ? B 18 ? B 44 ? 1 B G 2 1_555 B C 28 1_555 B C 3 1_555 B G 27 1_555 1.097 -0.061 4.443 4.234 0.852 38.784 -0.233 -0.940 4.531 1.278 -6.351 39.015 2 BB_G18C19:G43C44_BB B 18 ? B 44 ? B 19 ? B 43 ? 1 B C 3 1_555 B G 27 1_555 B A 4 1_555 B U 26 1_555 0.359 0.145 3.817 -7.419 28.330 41.776 -2.224 -1.046 3.209 35.053 9.179 50.640 3 BB_C19A20:U42G43_BB B 19 ? B 43 ? B 20 ? B 42 ? 1 B A 4 1_555 B U 26 1_555 B G 5 1_555 B C 25 1_555 -0.218 -0.256 4.696 2.339 -4.169 32.416 0.580 0.966 4.665 -7.418 -4.161 32.758 4 BB_A20G21:C41U42_BB B 20 ? B 42 ? B 21 ? B 41 ? 1 B G 5 1_555 B C 25 1_555 B A 6 1_555 B U 24 1_555 -0.454 -0.588 3.678 6.551 12.805 39.956 -2.241 1.358 3.240 18.046 -9.232 42.366 5 BB_G21A22:U40C41_BB B 21 ? B 41 ? B 22 ? B 40 ? 1 B A 6 1_555 B U 24 1_555 B G 10 1_555 B C 23 1_555 -1.173 -0.514 3.671 -9.789 6.748 41.593 -1.461 0.486 3.719 9.277 13.458 43.186 6 BB_A22G26:C39U40_BB B 22 ? B 40 ? B 26 ? B 39 ? 1 B G 10 1_555 B C 23 1_555 B A 11 1_555 B U 22 1_555 -0.729 -1.611 3.608 0.148 -7.465 20.860 -0.824 1.965 3.933 -19.817 -0.393 22.142 7 BB_G26A27:U38C39_BB B 26 ? B 39 ? B 27 ? B 38 ? 1 B A 11 1_555 B U 22 1_555 B G 12 1_555 B C 21 1_555 -0.443 -1.909 2.784 -2.973 10.224 44.272 -3.186 0.365 2.334 13.338 3.879 45.472 8 BB_A27G28:C37U38_BB B 27 ? B 38 ? B 28 ? B 37 ? 1 B G 12 1_555 B C 21 1_555 B C 13 1_555 B G 20 1_555 -0.151 -1.576 3.110 -5.200 8.572 22.800 -5.904 -1.012 2.349 20.460 12.413 24.880 9 BB_G28C29:G36C37_BB B 28 ? B 37 ? B 29 ? B 36 ? #