data_1UUD # _entry.id 1UUD # _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 1UUD PDBE EBI-14236 WWPDB D_1290014236 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1UTS unspecified 'DESIGNED HIV-1 TAR BINDING LIGAND' PDB 1UUI unspecified 'DESIGNED HIV-1 TAR BINDING LIGAND' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1UUD _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2003-12-18 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Davis, B.' 1 'Afshar, M.' 2 'Varani, G.' 3 'Karn, J.' 4 'Murchie, A.I.H.' 5 'Lentzen, G.' 6 'Drysdale, M.J.' 7 'Potter, A.J.' 8 'Bower, J.' 9 'Aboul-Ela, F.' 10 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Rational Design of Inhibitors of HIV-1 Tar RNA Through the Stabilisation of Electrostatic "Hot Spots" ; J.Mol.Biol. 336 343 ? 2004 JMOBAK UK 0022-2836 0070 ? 14757049 10.1016/J.JMB.2003.12.046 1 'The Structure of the Human Immunodeficiency Virus Recognition by Tat Protein' J.Mol.Biol. 253 313 ? 1995 JMOBAK UK 0022-2836 0070 ? 7563092 10.1006/JMBI.1995.0555 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Davis, B.' 1 primary 'Afshar, M.' 2 primary 'Varani, G.' 3 primary 'Murchie, A.I.H.' 4 primary 'Karn, J.' 5 primary 'Lentzen, G.' 6 primary 'Drysdale, M.J.' 7 primary 'Bower, J.' 8 primary 'Potter, A.J.' 9 primary 'Aboul-Ela, F.' 10 1 'Aboul-Ela, F.' 11 1 'Jkarn, J.' 12 1 'Varani, G.' 13 # _cell.entry_id 1UUD _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 1UUD _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 ;RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3') ; 9307.555 1 ? ? ? ;BULGED STEM LOOP REGION FROM 5'LTR OF HIV-1 MRNA-BINDING SITE FOR TRANSCRIPTIONAL ACTIVATOR PROTEIN TAT. ; 2 non-polymer syn 'N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE' 353.463 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'HIV-1 TAR RNA' # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGCAGAUCUGAGCCUGGGAGCUCUCUGCC _entity_poly.pdbx_seq_one_letter_code_can GGCAGAUCUGAGCCUGGGAGCUCUCUGCC _entity_poly.pdbx_strand_id B _entity_poly.pdbx_target_identifier ? # 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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'HUMAN IMMUNODEFICIENCY VIRUS 1 (CLONE 12)' _pdbx_entity_src_syn.organism_common_name HIV-1 _pdbx_entity_src_syn.ncbi_taxonomy_id 11706 _pdbx_entity_src_syn.details '29 NUCLEOTIDE SEQUENCE COMPRISING PRIMARY BINDING SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA POLYMERASE OFF OF A DNA TEMPLATE' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1UUD _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 1UUD _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1UUD _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1UUD _struct_ref_seq.db_align_beg 17 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 45 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 17 _struct_ref_seq.pdbx_auth_seq_align_end 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 P14 non-polymer . 'N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE' 'RBT203 INHIBITOR' 'C16 H31 N7 O2 2' 353.463 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 TOCSY 1 3 1 COSY 1 4 1 ROESY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 20 _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength 1 DRX Bruker 800 2 DRX Bruker 600 3 DMX Bruker 600 4 AMX Bruker 500 # _pdbx_nmr_refine.entry_id 1UUD _pdbx_nmr_refine.method 'NOE-RESTRAINED DYNAMICS' _pdbx_nmr_refine.details ;REFINEMENT INCLUDED A NUMBER OF MODELLING CONSTRAINTS BASED UPON PREVIOUSLY PUBLISHED DATA, AS WELL AS FINAL GENTLE REFINEMENT STEP USING CHARMM. DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1UUD _pdbx_nmr_details.text ;THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR SPECTRA FOR THE RNA AS ABOUND BY THE LIGAND RBT203 SHOWED SIMILAR NOE AND CHEMICAL SHIFT PATTERNS TO THE LATTER ; # _pdbx_nmr_ensemble.entry_id 1UUD _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST RESTRRAINT VIOLATION ENERGY' # _pdbx_nmr_representative.entry_id 1UUD _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR ? BRUNGER 1 'structure solution' XPLOR/CHARMM ? ? 2 # _exptl.entry_id 1UUD _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1UUD _struct.title 'NMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA' _struct.pdbx_descriptor '29-MER, N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'MINIMIZED AVERAGE' # _struct_keywords.entry_id 1UUD _struct_keywords.pdbx_keywords HIV-1 _struct_keywords.text 'HIV-1, TAR RNA, DRUG DESIGN, LIGAND-RNA INTERACTION, RNA BULGE' # 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 # 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 29 N3 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? B G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 28 N3 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 28 O2 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 28 N4 ? ? B G 18 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 27 N1 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 27 O6 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 27 N2 ? ? B C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 26 N3 ? ? B A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 26 O4 ? ? B A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 25 N3 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 25 O2 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 25 N4 ? ? B G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 24 N3 ? ? B A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 24 O4 ? ? B A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 11 N7 ? ? B U 23 B A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 11 N6 ? ? B U 23 B A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? B G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 22 N3 ? ? B A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 22 O4 ? ? B A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? B G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 20 N1 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 20 O6 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 20 N2 ? ? B C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE P14 B1046' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 A A 6 ? A B 22 . ? 1_555 ? 2 AC1 9 U A 7 ? U B 23 . ? 1_555 ? 3 AC1 9 G A 10 ? G B 26 . ? 1_555 ? 4 AC1 9 A A 11 ? A B 27 . ? 1_555 ? 5 AC1 9 G A 12 ? G B 28 . ? 1_555 ? 6 AC1 9 A A 19 ? A B 35 . ? 1_555 ? 7 AC1 9 G A 20 ? G B 36 . ? 1_555 ? 8 AC1 9 C A 21 ? C B 37 . ? 1_555 ? 9 AC1 9 U A 22 ? U B 38 . ? 1_555 ? # _database_PDB_matrix.entry_id 1UUD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1UUD _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 G 1 17 17 G G B . n A 1 2 G 2 18 18 G G B . n A 1 3 C 3 19 19 C C B . n A 1 4 A 4 20 20 A A B . n A 1 5 G 5 21 21 G G B . n A 1 6 A 6 22 22 A A B . n A 1 7 U 7 23 23 U U B . n A 1 8 C 8 24 24 C C B . n A 1 9 U 9 25 25 U U B . n A 1 10 G 10 26 26 G G B . n A 1 11 A 11 27 27 A A B . n A 1 12 G 12 28 28 G G B . n A 1 13 C 13 29 29 C C B . n A 1 14 C 14 30 30 C C B . n A 1 15 U 15 31 31 U U B . n A 1 16 G 16 32 32 G G B . n A 1 17 G 17 33 33 G G B . n A 1 18 G 18 34 34 G G B . n A 1 19 A 19 35 35 A A B . n A 1 20 G 20 36 36 G G B . n A 1 21 C 21 37 37 C C B . n A 1 22 U 22 38 38 U U B . n A 1 23 C 23 39 39 C C B . n A 1 24 U 24 40 40 U U B . n A 1 25 C 25 41 41 C C B . n A 1 26 U 26 42 42 U U B . n A 1 27 G 27 43 43 G G B . n A 1 28 C 28 44 44 C C B . n A 1 29 C 29 45 45 C C B . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id P14 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1046 _pdbx_nonpoly_scheme.auth_seq_num 1046 _pdbx_nonpoly_scheme.pdb_mon_id P14 _pdbx_nonpoly_scheme.auth_mon_id P14 _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 2004-03-15 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 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 ? # 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' 'Version format compliance' # 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 N7 B G 17 ? ? C8 B G 17 ? ? N9 B G 17 ? ? 117.65 113.10 4.55 0.50 N 2 1 C8 B G 17 ? ? N9 B G 17 ? ? C4 B G 17 ? ? 103.71 106.40 -2.69 0.40 N 3 1 N7 B G 18 ? ? C8 B G 18 ? ? N9 B G 18 ? ? 117.70 113.10 4.60 0.50 N 4 1 C8 B G 18 ? ? N9 B G 18 ? ? C4 B G 18 ? ? 103.75 106.40 -2.65 0.40 N 5 1 N7 B A 20 ? ? C8 B A 20 ? ? N9 B A 20 ? ? 117.55 113.80 3.75 0.50 N 6 1 N7 B G 21 ? ? C8 B G 21 ? ? N9 B G 21 ? ? 117.65 113.10 4.55 0.50 N 7 1 C8 B G 21 ? ? N9 B G 21 ? ? C4 B G 21 ? ? 103.71 106.40 -2.69 0.40 N 8 1 N7 B A 22 ? ? C8 B A 22 ? ? N9 B A 22 ? ? 117.52 113.80 3.72 0.50 N 9 1 N7 B G 26 ? ? C8 B G 26 ? ? N9 B G 26 ? ? 117.57 113.10 4.47 0.50 N 10 1 C8 B G 26 ? ? N9 B G 26 ? ? C4 B G 26 ? ? 103.74 106.40 -2.66 0.40 N 11 1 N7 B A 27 ? ? C8 B A 27 ? ? N9 B A 27 ? ? 117.48 113.80 3.68 0.50 N 12 1 N7 B G 28 ? ? C8 B G 28 ? ? N9 B G 28 ? ? 117.59 113.10 4.49 0.50 N 13 1 C8 B G 28 ? ? N9 B G 28 ? ? C4 B G 28 ? ? 103.79 106.40 -2.61 0.40 N 14 1 N7 B G 32 ? ? C8 B G 32 ? ? N9 B G 32 ? ? 117.65 113.10 4.55 0.50 N 15 1 C8 B G 32 ? ? N9 B G 32 ? ? C4 B G 32 ? ? 103.80 106.40 -2.60 0.40 N 16 1 N7 B G 33 ? ? C8 B G 33 ? ? N9 B G 33 ? ? 117.69 113.10 4.59 0.50 N 17 1 C8 B G 33 ? ? N9 B G 33 ? ? C4 B G 33 ? ? 103.68 106.40 -2.72 0.40 N 18 1 N7 B G 34 ? ? C8 B G 34 ? ? N9 B G 34 ? ? 117.65 113.10 4.55 0.50 N 19 1 C8 B G 34 ? ? N9 B G 34 ? ? C4 B G 34 ? ? 103.74 106.40 -2.66 0.40 N 20 1 N7 B A 35 ? ? C8 B A 35 ? ? N9 B A 35 ? ? 117.59 113.80 3.79 0.50 N 21 1 N7 B G 36 ? ? C8 B G 36 ? ? N9 B G 36 ? ? 117.80 113.10 4.70 0.50 N 22 1 C8 B G 36 ? ? N9 B G 36 ? ? C4 B G 36 ? ? 103.77 106.40 -2.63 0.40 N 23 1 N7 B G 43 ? ? C8 B G 43 ? ? N9 B G 43 ? ? 117.64 113.10 4.54 0.50 N 24 1 C8 B G 43 ? ? N9 B G 43 ? ? C4 B G 43 ? ? 103.76 106.40 -2.64 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1UUD 'double helix' 1UUD 'a-form double helix' 1UUD 'hairpin loop' 1UUD 'bulge 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 A G 1 1_555 A C 29 1_555 -2.015 -0.548 0.129 -0.440 -3.530 -1.968 1 B_G17:C45_B B 17 ? B 45 ? 19 1 1 A G 2 1_555 A C 28 1_555 -0.992 -0.458 -0.197 -3.510 -2.042 -7.224 2 B_G18:C44_B B 18 ? B 44 ? 19 1 1 A C 3 1_555 A G 27 1_555 0.764 -0.386 -0.015 -4.468 -2.513 -4.291 3 B_C19:G43_B B 19 ? B 43 ? 19 1 1 A A 4 1_555 A U 26 1_555 -0.628 -0.302 0.374 -3.618 -4.694 7.958 4 B_A20:U42_B B 20 ? B 42 ? 20 1 1 A G 5 1_555 A C 25 1_555 0.208 -0.114 -0.899 -18.940 -3.276 -8.710 5 B_G21:C41_B B 21 ? B 41 ? 19 1 1 A A 6 1_555 A U 24 1_555 1.072 0.161 -0.508 -12.122 15.850 -23.036 6 B_A22:U40_B B 22 ? B 40 ? 20 1 1 A G 10 1_555 A C 23 1_555 -0.557 -0.125 -0.948 -35.292 -3.507 -3.222 7 B_G26:C39_B B 26 ? B 39 ? 19 1 1 A A 11 1_555 A U 22 1_555 0.319 0.106 0.311 -8.287 -2.046 -10.465 8 B_A27:U38_B B 27 ? B 38 ? 20 1 1 A G 12 1_555 A C 21 1_555 -0.289 -0.246 -0.469 -6.827 5.164 -2.394 9 B_G28:C37_B B 28 ? B 37 ? 19 1 1 A C 13 1_555 A G 20 1_555 1.266 -0.480 -0.044 -11.437 -0.109 -5.385 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 A G 1 1_555 A C 29 1_555 A G 2 1_555 A C 28 1_555 -1.003 -1.165 3.794 -1.732 -1.383 39.762 -1.522 1.238 3.869 -2.032 2.544 39.822 1 BB_G17G18:C44C45_BB B 17 ? B 45 ? B 18 ? B 44 ? 1 A G 2 1_555 A C 28 1_555 A C 3 1_555 A G 27 1_555 -0.198 -1.078 3.498 -1.428 17.427 41.598 -3.003 0.128 2.854 23.338 1.913 44.973 2 BB_G18C19:G43C44_BB B 18 ? B 44 ? B 19 ? B 43 ? 1 A C 3 1_555 A G 27 1_555 A A 4 1_555 A U 26 1_555 1.270 -1.930 2.794 -4.203 13.517 24.470 -6.095 -3.269 1.332 28.996 9.017 28.216 3 BB_C19A20:U42G43_BB B 19 ? B 43 ? B 20 ? B 42 ? 1 A A 4 1_555 A U 26 1_555 A G 5 1_555 A C 25 1_555 0.260 -1.478 3.713 6.217 19.309 39.373 -3.874 0.267 2.746 26.624 -8.573 44.106 4 BB_A20G21:C41U42_BB B 20 ? B 42 ? B 21 ? B 41 ? 1 A G 5 1_555 A C 25 1_555 A A 6 1_555 A U 24 1_555 -1.033 -1.893 3.426 -1.261 -0.987 35.971 -2.914 1.482 3.508 -1.596 2.041 36.005 5 BB_G21A22:U40C41_BB B 21 ? B 41 ? B 22 ? B 40 ? 1 A A 6 1_555 A U 24 1_555 A G 10 1_555 A C 23 1_555 -0.872 -1.577 5.279 7.098 24.701 41.382 -4.777 1.884 3.657 31.569 -9.072 48.414 6 BB_A22G26:C39U40_BB B 22 ? B 40 ? B 26 ? B 39 ? 1 A G 10 1_555 A C 23 1_555 A A 11 1_555 A U 22 1_555 -0.048 -0.952 2.800 -5.108 -1.921 39.323 -1.208 -0.444 2.826 -2.839 7.546 39.685 7 BB_G26A27:U38C39_BB B 26 ? B 39 ? B 27 ? B 38 ? 1 A A 11 1_555 A U 22 1_555 A G 12 1_555 A C 21 1_555 -0.137 -2.407 3.972 -1.837 -14.597 18.975 1.160 -0.547 4.616 -37.770 4.754 23.969 8 BB_A27G28:C37U38_BB B 27 ? B 38 ? B 28 ? B 37 ? 1 A G 12 1_555 A C 21 1_555 A C 13 1_555 A G 20 1_555 -0.173 -1.564 3.304 0.834 29.363 42.489 -3.598 0.250 1.911 35.866 -1.019 51.265 9 BB_G28C29:G36C37_BB B 28 ? B 37 ? B 29 ? B 36 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE' _pdbx_entity_nonpoly.comp_id P14 #