data_2KX5 # _entry.id 2KX5 # _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 2KX5 RCSB RCSB101683 WWPDB D_1000101683 # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2KDQ PDB 'HIV-1 and peptide mimic of Tat protein' unspecified 2A9X PDB 'BIV TAR and BIV Tat mimic' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KX5 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-04-26 _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.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Davidson, A.' 1 'Patora-Komisarska, K.' 2 'Robinson, J.' 3 'Varani, G.' 4 # _citation.id primary _citation.title 'Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 39 _citation.page_first 248 _citation.page_last 256 _citation.year 2011 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20724442 _citation.pdbx_database_id_DOI 10.1093/nar/gkq713 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Davidson, A.' 1 primary 'Patora-Komisarska, K.' 2 primary 'Robinson, J.A.' 3 primary 'Varani, G.' 4 # 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 'HIV TAR RNA' 9307.555 1 ? ? 'HIV-1 TAR RNA hairpin' ? 2 polymer syn 'Cyclic peptide mimetic of Tat protein' 2271.852 1 ? 'D-Pro at position 17' KP-Z-41 ? # 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 polyribonucleotide no no GGCAGAUCUGAGCCUGGGAGCUCUCUGCC GGCAGAUCUGAGCCUGGGAGCUCUCUGCC A ? 2 'polypeptide(L)' no yes 'RVRCRQRKGRRICIRI(DPR)P' RVRCRQRKGRRICIRIPP B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 A n 1 5 G n 1 6 A n 1 7 U n 1 8 C n 1 9 U n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 C n 1 15 U n 1 16 G n 1 17 G n 1 18 G n 1 19 A n 1 20 G n 1 21 C n 1 22 U n 1 23 C n 1 24 U n 1 25 C n 1 26 U n 1 27 G n 1 28 C n 1 29 C n 2 1 ARG n 2 2 VAL n 2 3 ARG n 2 4 CYS n 2 5 ARG n 2 6 GLN n 2 7 ARG n 2 8 LYS n 2 9 GLY n 2 10 ARG n 2 11 ARG n 2 12 ILE n 2 13 CYS n 2 14 ILE n 2 15 ARG n 2 16 ILE n 2 17 DPR n 2 18 PRO 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 2KX5 2KX5 1 ? GGCAGAUCUGAGCCUGGGAGCUCUCUGCC ? 2 PDB 2KX5 2KX5 2 ? RVRCRQRKGRRICIRIPP ? # 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 2KX5 A 1 ? 29 ? 2KX5 17 ? 45 ? 17 45 2 2 2KX5 B 1 ? 18 ? 2KX5 1 ? 18 ? 1 18 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 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 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 2 1 1 '2D 1H-1H TOCSY' 2 2 3 '2D 1H-1H COSY' 2 3 1 '2D 1H-1H NOESY' 2 4 3 '3D HCCH-TOCSY' 2 5 3 '3D 1H-13C NOESY' 1 6 2 '2D 1H-1H NOESY' 2 7 4 '2D 1H-1H NOESY' 2 8 3 '2D F1fF2f NOESY' 1 9 5 '2D F1fF2f NOESY' 2 10 3 '2D F1fF2f TOCSY' # 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 0.01 6.6 ambient ? 277 K 2 0.01 6.6 ambient ? 298 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1 mM HIV-1 TAR/KP-Z-41-1, 100% D2O' 1 '100% D2O' '1 mM HIV-1 TAR/KP-Z-41-2, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '1 mM [U-98% 13C; U-98% 15N] HIV-1 TAR/KP-Z-41-3, 100% D2O' 3 '100% D2O' '1 mM [U-2H] HIV-1 TAR/KP-Z-41-4, 100% D2O' 4 '100% D2O' '1 mM [U-98% 13C; U-98% 15N] HIV-1 TAR/KP-Z-41-5, 90% H2O/10% D2O' 5 '90% H2O/10% 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' # _pdbx_nmr_refine.entry_id 2KX5 _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 'structures with the least restraint violations and lowest energy' _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 2KX5 _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 2KX5 _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 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' X-PLOR_NIH ? 1 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 2 Goddard 'chemical shift assignment' SPARKY ? 3 Goddard 'peak picking' SPARKY ? 4 'Schwieters, Kuszewski, Tjandra and Clore' refinement X-PLOR_NIH ? 5 # _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 2KX5 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KX5 _struct.title 'Recognition of HIV TAR RNA by peptide mimetic of Tat protein' _struct.pdbx_descriptor 'Cyclic peptide mimetic of Tat protein/HIV Tar RNA Complex' _struct.pdbx_model_details 'lowest energy, model 8' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KX5 _struct_keywords.pdbx_keywords 'RNA binding protein/RNA' _struct_keywords.text 'HIV-1 TAR, Tat, RNA recognition, immunodeficiency virus; TAR RNA, 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 disulf1 disulf ? ? B CYS 4 SG ? ? ? 1_555 B CYS 13 SG ? ? B CYS 4 B CYS 13 1_555 ? ? ? ? ? ? ? 2.019 ? covale1 covale ? ? B DPR 17 C ? ? ? 1_555 B PRO 18 N ? ? B DPR 17 B PRO 18 1_555 ? ? ? ? ? ? ? 1.302 ? covale2 covale ? ? B ARG 1 N ? ? ? 1_555 B PRO 18 C ? ? B ARG 1 B PRO 18 1_555 ? ? ? ? ? ? ? 1.334 ? covale3 covale ? ? B ILE 16 C ? ? ? 1_555 B DPR 17 N ? ? B ILE 16 B DPR 17 1_555 ? ? ? ? ? ? ? 1.309 ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 18 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 18 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 18 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 26 N3 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 26 O4 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 A G 10 O6 ? ? A A 22 A G 26 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? hydrog16 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 11 N7 ? ? A U 23 A A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog19 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 11 N6 ? ? A U 23 A A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog20 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A A 11 N6 ? ? ? 1_555 A C 23 N3 ? ? A A 27 A C 39 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? hydrog26 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? 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 B 2 ? ARG B 7 ? VAL B 2 ARG B 7 A 2 ARG B 10 ? ARG B 15 ? ARG B 10 ARG B 15 # _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 B _pdbx_struct_sheet_hbond.range_1_label_seq_id 7 _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 B _pdbx_struct_sheet_hbond.range_1_auth_seq_id 7 _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 B _pdbx_struct_sheet_hbond.range_2_label_seq_id 10 _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 B _pdbx_struct_sheet_hbond.range_2_auth_seq_id 10 # _atom_sites.entry_id 2KX5 _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 S # 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 G 1 17 17 G G A . n A 1 2 G 2 18 18 G G A . n A 1 3 C 3 19 19 C C A . n A 1 4 A 4 20 20 A A A . n A 1 5 G 5 21 21 G G A . n A 1 6 A 6 22 22 A A A . n A 1 7 U 7 23 23 U U A . n A 1 8 C 8 24 24 C C A . n A 1 9 U 9 25 25 U U A . n A 1 10 G 10 26 26 G G A . n A 1 11 A 11 27 27 A A A . n A 1 12 G 12 28 28 G G A . n A 1 13 C 13 29 29 C C A . n A 1 14 C 14 30 30 C C A . n A 1 15 U 15 31 31 U U A . n A 1 16 G 16 32 32 G G A . n A 1 17 G 17 33 33 G G A . n A 1 18 G 18 34 34 G G A . n A 1 19 A 19 35 35 A A A . n A 1 20 G 20 36 36 G G A . n A 1 21 C 21 37 37 C C A . n A 1 22 U 22 38 38 U U A . n A 1 23 C 23 39 39 C C A . n A 1 24 U 24 40 40 U U A . n A 1 25 C 25 41 41 C C A . n A 1 26 U 26 42 42 U U A . n A 1 27 G 27 43 43 G G A . n A 1 28 C 28 44 44 C C A . n A 1 29 C 29 45 45 C C A . n B 2 1 ARG 1 1 1 ARG ARG B . n B 2 2 VAL 2 2 2 VAL VAL B . n B 2 3 ARG 3 3 3 ARG ARG B . n B 2 4 CYS 4 4 4 CYS CYS B . n B 2 5 ARG 5 5 5 ARG ARG B . n B 2 6 GLN 6 6 6 GLN GLN B . n B 2 7 ARG 7 7 7 ARG ARG B . n B 2 8 LYS 8 8 8 LYS LYS B . n B 2 9 GLY 9 9 9 GLY GLY B . n B 2 10 ARG 10 10 10 ARG ARG B . n B 2 11 ARG 11 11 11 ARG ARG B . n B 2 12 ILE 12 12 12 ILE ILE B . n B 2 13 CYS 13 13 13 CYS CYS B . n B 2 14 ILE 14 14 14 ILE ILE B . n B 2 15 ARG 15 15 15 ARG ARG B . n B 2 16 ILE 16 16 16 ILE ILE B . n B 2 17 DPR 17 17 17 DPR DPR B . n B 2 18 PRO 18 18 18 PRO PRO 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 2010-07-07 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 'HIV-1 TAR/KP-Z-41-1' 1 ? mM ? 1 'HIV-1 TAR/KP-Z-41-2' 1 ? mM ? 2 'HIV-1 TAR/KP-Z-41-3' 1 ? mM '[U-98% 13C; U-98% 15N]' 3 'HIV-1 TAR/KP-Z-41-4' 1 ? mM '[U-2H]' 4 'HIV-1 TAR/KP-Z-41-5' 1 ? mM '[U-98% 13C; U-98% 15N]' 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 OP1 A C 24 ? ? "H2'" A U 25 ? ? 1.56 2 1 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.58 3 2 H22 A G 32 ? ? "O2'" A G 33 ? ? 1.57 4 2 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.59 5 2 O B ARG 7 ? ? O B ARG 10 ? ? 2.14 6 4 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.56 7 6 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.56 8 7 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.55 9 7 OP1 A C 24 ? ? "H2'" A U 25 ? ? 1.56 10 8 "HO2'" A G 32 ? ? "O5'" A G 33 ? ? 1.44 11 8 "H4'" A U 23 ? ? OP1 A G 26 ? ? 1.59 # 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 2 "C4'" A G 43 ? ? "C3'" A G 43 ? ? 1.628 1.527 0.101 0.011 N 2 5 "C4'" A G 43 ? ? "C3'" A G 43 ? ? 1.601 1.527 0.074 0.011 N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 2 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 43 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C4'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 43 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 43 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 97.97 _pdbx_validate_rmsd_angle.angle_target_value 104.00 _pdbx_validate_rmsd_angle.angle_deviation -6.03 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.00 _pdbx_validate_rmsd_angle.linker_flag 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 1 DPR B 17 ? ? 30.65 -94.09 2 2 LYS B 8 ? ? 32.96 45.32 3 2 DPR B 17 ? ? 28.76 -90.74 4 4 DPR B 17 ? ? 28.47 -92.18 5 5 DPR B 17 ? ? 28.86 -92.30 6 6 DPR B 17 ? ? 30.10 -94.47 7 7 LYS B 8 ? ? 36.65 45.12 8 7 DPR B 17 ? ? 38.44 -130.20 9 8 DPR B 17 ? ? 30.29 -94.61 10 9 LYS B 8 ? ? 60.31 64.13 11 9 DPR B 17 ? ? 38.53 -128.63 12 10 DPR B 17 ? ? 30.00 -94.89 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 C A 39 ? ? 0.080 'SIDE CHAIN' 2 2 C A 39 ? ? 0.078 'SIDE CHAIN' 3 3 C A 39 ? ? 0.068 'SIDE CHAIN' 4 4 C A 39 ? ? 0.073 'SIDE CHAIN' 5 5 C A 39 ? ? 0.078 'SIDE CHAIN' 6 6 C A 39 ? ? 0.085 'SIDE CHAIN' 7 7 C A 39 ? ? 0.071 'SIDE CHAIN' 8 8 C A 39 ? ? 0.066 'SIDE CHAIN' 9 9 C A 39 ? ? 0.071 'SIDE CHAIN' 10 10 C A 39 ? ? 0.074 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KX5 'a-form double helix' 2KX5 'quadruple 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 G 1 1_555 A C 29 1_555 0.046 -0.077 0.152 0.314 -0.359 -1.510 1 A_G17:C45_A A 17 ? A 45 ? 19 1 1 A G 2 1_555 A C 28 1_555 -0.193 -0.115 0.009 1.274 -8.029 -0.982 2 A_G18:C44_A A 18 ? A 44 ? 19 1 1 A C 3 1_555 A G 27 1_555 -0.152 -0.089 -0.011 1.603 -13.478 -0.430 3 A_C19:G43_A A 19 ? A 43 ? 19 1 1 A A 4 1_555 A U 26 1_555 0.358 -0.180 0.143 -5.013 -16.947 -2.407 4 A_A20:U42_A A 20 ? A 42 ? 20 1 1 A G 5 1_555 A C 25 1_555 0.128 -0.130 0.184 -8.264 -16.439 -2.686 5 A_G21:C41_A A 21 ? A 41 ? 19 1 1 A A 6 1_555 A U 24 1_555 0.342 -0.217 0.372 -10.827 -23.367 -11.280 6 A_A22:U40_A A 22 ? A 40 ? 20 1 1 A G 10 1_555 A C 23 1_555 0.142 -0.225 -1.146 -20.732 -17.795 6.403 7 A_G26:C39_A A 26 ? A 39 ? 19 1 1 A A 11 1_555 A U 22 1_555 0.277 -0.152 -0.020 -8.394 -1.800 1.057 8 A_A27:U38_A A 27 ? A 38 ? 20 1 1 A G 12 1_555 A C 21 1_555 -0.420 -0.170 0.073 -5.455 1.649 -1.108 9 A_G28:C37_A A 28 ? A 37 ? 19 1 1 A C 13 1_555 A G 20 1_555 0.472 -0.229 0.467 0.715 -3.908 -4.191 10 A_C29:G36_A A 29 ? A 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 A G 1 1_555 A C 29 1_555 A G 2 1_555 A C 28 1_555 -0.007 -1.928 3.346 0.847 12.798 25.686 -6.466 0.185 2.158 26.765 -1.772 28.662 1 AA_G17G18:C44C45_AA A 17 ? A 45 ? A 18 ? A 44 ? 1 A G 2 1_555 A C 28 1_555 A C 3 1_555 A G 27 1_555 0.036 -1.794 3.318 0.085 9.609 28.444 -5.304 -0.054 2.587 18.886 -0.167 29.991 2 AA_G18C19:G43C44_AA A 18 ? A 44 ? A 19 ? A 43 ? 1 A C 3 1_555 A G 27 1_555 A A 4 1_555 A U 26 1_555 -0.086 -1.567 3.555 -0.202 8.799 31.384 -4.367 0.118 3.017 15.878 0.364 32.565 3 AA_C19A20:U42G43_AA A 19 ? A 43 ? A 20 ? A 42 ? 1 A A 4 1_555 A U 26 1_555 A G 5 1_555 A C 25 1_555 0.056 -1.741 3.205 0.761 12.628 29.139 -5.220 0.021 2.274 23.739 -1.431 31.712 4 AA_A20G21:C41U42_AA A 20 ? A 42 ? A 21 ? A 41 ? 1 A G 5 1_555 A C 25 1_555 A A 6 1_555 A U 24 1_555 -0.098 -1.425 3.337 0.672 11.954 33.844 -3.946 0.252 2.694 19.782 -1.111 35.841 5 AA_G21A22:U40C41_AA A 21 ? A 41 ? A 22 ? A 40 ? 1 A A 6 1_555 A U 24 1_555 A G 10 1_555 A C 23 1_555 -1.500 -1.762 2.909 2.589 16.373 51.328 -2.771 1.789 2.218 18.363 -2.903 53.765 6 AA_A22G26:C39U40_AA A 22 ? A 40 ? A 26 ? A 39 ? 1 A G 10 1_555 A C 23 1_555 A A 11 1_555 A U 22 1_555 -0.603 -2.060 2.648 -6.899 10.392 21.714 -6.924 -0.045 1.623 25.095 16.661 25.004 7 AA_G26A27:U38C39_AA A 26 ? A 39 ? A 27 ? A 38 ? 1 A A 11 1_555 A U 22 1_555 A G 12 1_555 A C 21 1_555 -0.262 -2.093 3.638 -0.915 2.469 22.883 -6.178 0.310 3.403 6.196 2.296 23.032 8 AA_A27G28:C37U38_AA A 27 ? A 38 ? A 28 ? A 37 ? 1 A G 12 1_555 A C 21 1_555 A C 13 1_555 A G 20 1_555 -0.286 -1.714 3.374 -1.831 8.184 30.606 -4.595 0.197 2.844 15.150 3.390 31.707 9 AA_G28C29:G36C37_AA A 28 ? A 37 ? A 29 ? A 36 ? #