data_2KMJ # _entry.id 2KMJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 2KMJ pdb_00002kmj 10.2210/pdb2kmj/pdb RCSB RCSB101305 ? ? WWPDB D_1000101305 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KMJ _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-07-30 _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 'Ferner, J.' 1 'Suhartono, M.' 2 'Breitung, S.' 3 'Jonker, H.R.A.' 4 'Hennig, M.' 5 'Woehnert, J.' 6 'Goebel, M.' 7 'Schwalbe, H.' 8 # _citation.id primary _citation.title 'Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries.' _citation.journal_abbrev Chembiochem _citation.journal_volume 10 _citation.page_first 1490 _citation.page_last 1494 _citation.year 2009 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1439-4227 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19444830 _citation.pdbx_database_id_DOI 10.1002/cbic.200900220 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ferner, J.' 1 ? primary 'Suhartono, M.' 2 ? primary 'Breitung, S.' 3 ? primary 'Jonker, H.R.A.' 4 ? primary 'Hennig, M.' 5 ? primary 'Wohnert, J.' 6 ? primary 'Gobel, M.' 7 ? primary 'Schwalbe, H.' 8 ? # 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 man 'RNA (28-MER)' 8940.293 1 ? ? ? 'UUCG-TAR RNA' 2 polymer syn Pyrimidinylpeptide 507.613 2 ? ? ? ? # 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 GGCCAGAUUGAGCUUCGGCUCUCUGGUC GGCCAGAUUGAGCUUCGGCUCUCUGGUC A ? 2 'polypeptide(D)' no yes '(DAR)(ZUK)(DAR)(NH2)' RXRX B,C ? # 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 C n 1 5 A n 1 6 G n 1 7 A n 1 8 U n 1 9 U n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 U n 1 15 U n 1 16 C n 1 17 G n 1 18 G n 1 19 C n 1 20 U n 1 21 C n 1 22 U n 1 23 C n 1 24 U n 1 25 G n 1 26 G n 1 27 U n 1 28 C n 2 1 DAR n 2 2 ZUK n 2 3 DAR n 2 4 NH2 n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Human immunodeficiency virus 2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 11709 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name puc19 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Synthetic peptide' # 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 2KMJ 2KMJ 1 GGCCAGAUUGAGCUUCGGCUCUCUGGUC 16 ? 2 PDB 2KMJ 2KMJ 2 RLR 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 2KMJ A 1 ? 28 ? 2KMJ 16 ? 46 ? 16 46 2 2 2KMJ B 1 ? 4 ? 2KMJ 1 ? 4 ? 1 4 3 2 2KMJ C 1 ? 4 ? 2KMJ 1 ? 4 ? 1 4 # 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 DAR 'D-peptide linking' . D-ARGININE ? 'C6 H15 N4 O2 1' 175.209 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 ZUK 'D-peptide linking' . 5-pyrimidin-2-yl-D-norvaline ? 'C9 H13 N3 O2' 195.218 # 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-15N HSQC' 1 2 2 '2D 1H-13C HSQC' 1 3 3 '2D 1H-1H TOCSY' 1 4 3 '2D 1H-1H NOESY' 1 5 4 '2D 1H-1H NOESY' 1 6 2 '3D HCCH-TOCSY' 1 7 2 '3D HCCH-COSY' 2 8 1 '3D 1H-15N NOESY' 1 9 2 '3D 1H-13C NOESY' 1 10 2 '2D H(C)N' 1 11 2 '2D 1H-15N HSQC (2J)' 1 12 2 '2D 1H-13C HSQC' 2 13 1 '2D HNN-COSY' 1 14 2 '2D H5NN-COSY' 1 15 2 '3D forward-directed HCC-TOCSY-CCH E.COSY' 2 16 1 '2D 1H-15N CPMG-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 75 6.2 ambient ? 298 K 2 75 6.2 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8, 100% D2O ; 2 '100% D2O' '0.65 mM UUCG-TAR-9, 5.2 mM Pyrimidinylpeptide-10, 50 mM potassium chloride-11, 25 mM potassium phosphate-12, 90% H2O / 10% D2O' 3 '90% H2O/10% D2O' '0.65 mM UUCG-TAR-13, 5.2 mM Pyrimidinylpeptide-14, 50 mM potassium chloride-15, 25 mM potassium phosphate-16, 100% D2O' 4 '100% D2O' ;0.2 mM [U-100% 13C; U-100% 15N] UUCG-TAR-17, 0.8 mM Pyrimidinylpeptide-18, 50 mM potassium chloride-19, 25 mM potassium phosphate-20, 16 mg/mL Pf1 phage-21, 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 900 Bruker AVANCE 1 'Bruker Avance' 800 Bruker AVANCE 2 'Bruker Avance' 700 Bruker AVANCE 3 'Bruker Avance' 600 Bruker AVANCE 4 'Bruker Avance' 600 Bruker DRX 5 'Bruker DRX' 400 Bruker AVANCE 6 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KMJ _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 'Top-ranked ensemble' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KMJ _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 2KMJ _pdbx_nmr_representative.selection_criteria 'top-ranked ensemble' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TopSpin 2.1 1 'Bruker Biospin' processing TopSpin 2.1 2 'Bruker Biospin' 'data analysis' TopSpin 2.1 3 Goddard 'chemical shift assignment' Sparky 3.114 4 Goddard 'data analysis' Sparky 3.114 5 Goddard 'peak picking' Sparky 3.114 6 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.1 7 ;Linge, O'Donoghue and Nilges ; refinement ARIA 1.2 8 'Dominguez, Boelens and Bonvin' refinement HADDOCK 2.1 9 # _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 'High resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry' _exptl.entry_id 2KMJ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KMJ _struct.title 'High resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry' _struct.pdbx_model_details 'Top-ranked ensemble, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KMJ _struct_keywords.pdbx_keywords RNA/PEPTIDE _struct_keywords.text 'RNA-ligand complex, binding stoichiometry, HIV-2 TAR, RNA-PEPTIDE COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 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 ? B DAR 1 C ? ? ? 1_555 B ZUK 2 N ? ? B DAR 1 B ZUK 2 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale2 covale both ? B ZUK 2 C ? ? ? 1_555 B DAR 3 N ? ? B ZUK 2 B DAR 3 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale3 covale both ? B DAR 3 C ? ? ? 1_555 B NH2 4 N ? ? B DAR 3 B NH2 4 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale4 covale both ? C DAR 1 C ? ? ? 1_555 C ZUK 2 N ? ? C DAR 1 C ZUK 2 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale5 covale both ? C ZUK 2 C ? ? ? 1_555 C DAR 3 N ? ? C ZUK 2 C DAR 3 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale6 covale both ? C DAR 3 C ? ? ? 1_555 C NH2 4 N ? ? C DAR 3 C NH2 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 16 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 16 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 16 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 27 O2 ? ? A G 17 A U 45 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 27 N3 ? ? A G 17 A U 45 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 26 N1 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 26 N2 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 7 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 19 N3 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 19 O2 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 19 N4 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 O2 ? ? ? 1_555 A G 17 N1 ? ? A U 31 A G 34 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2KMJ _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 16 16 G G A . n A 1 2 G 2 17 17 G G A . n A 1 3 C 3 18 18 C C A . n A 1 4 C 4 19 19 C C A . n A 1 5 A 5 20 20 A A A . n A 1 6 G 6 21 21 G G A . n A 1 7 A 7 22 22 A A A . n A 1 8 U 8 23 23 U U 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 U 14 31 31 U U A . n A 1 15 U 15 32 32 U U A . n A 1 16 C 16 33 33 C C A . n A 1 17 G 17 34 34 G G A . n A 1 18 G 18 36 36 G G A . n A 1 19 C 19 37 37 C C A . n A 1 20 U 20 38 38 U U A . n A 1 21 C 21 39 39 C C A . n A 1 22 U 22 40 40 U U A . n A 1 23 C 23 41 41 C C A . n A 1 24 U 24 42 42 U U A . n A 1 25 G 25 43 43 G G A . n A 1 26 G 26 44 44 G G A . n A 1 27 U 27 45 45 U U A . n A 1 28 C 28 46 46 C C A . n B 2 1 DAR 1 1 1 DAR DAR B . n B 2 2 ZUK 2 2 2 ZUK ZUK B . n B 2 3 DAR 3 3 3 DAR DAR B . n B 2 4 NH2 4 4 4 NH2 NH2 B . n C 2 1 DAR 1 1 4 DAR DAR C . n C 2 2 ZUK 2 2 2 ZUK ZUK C . n C 2 3 DAR 3 3 3 DAR DAR C . n C 2 4 NH2 4 4 4 NH2 NH2 C . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-08-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 4 'Structure model' 2 0 2023-11-15 # _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' 5 4 'Structure model' 'Atomic model' 6 4 'Structure model' 'Data collection' # 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_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_ref_seq 8 4 'Structure model' atom_site 9 4 'Structure model' chem_comp_atom 10 4 'Structure model' chem_comp_bond # 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' '_pdbx_nmr_spectrometer.model' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_ref_seq.db_align_end' 7 4 'Structure model' '_atom_site.auth_atom_id' 8 4 'Structure model' '_atom_site.label_atom_id' # 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 UUCG-TAR-1 0.65 ? mM '[U-100% 13C; U-100% 15N]' 1 Pyrimidinylpeptide-2 5.2 ? mM ? 1 'potassium chloride-3' 50 ? mM ? 1 'potassium phosphate-4' 25 ? mM ? 1 UUCG-TAR-5 0.65 ? mM '[U-100% 13C; U-100% 15N]' 2 Pyrimidinylpeptide-6 5.2 ? mM ? 2 'potassium chloride-7' 50 ? mM ? 2 'potassium phosphate-8' 25 ? mM ? 2 UUCG-TAR-9 0.65 ? mM ? 3 Pyrimidinylpeptide-10 5.2 ? mM ? 3 'potassium chloride-11' 50 ? mM ? 3 'potassium phosphate-12' 25 ? mM ? 3 UUCG-TAR-13 0.65 ? mM ? 4 Pyrimidinylpeptide-14 5.2 ? mM ? 4 'potassium chloride-15' 50 ? mM ? 4 'potassium phosphate-16' 25 ? mM ? 4 UUCG-TAR-17 0.2 ? mM '[U-100% 13C; U-100% 15N]' 5 Pyrimidinylpeptide-18 0.8 ? mM ? 5 'potassium chloride-19' 50 ? mM ? 5 'potassium phosphate-20' 25 ? mM ? 5 'Pf1 phage-21' 16 ? mg/mL ? 5 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2KMJ _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 60 _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 4 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 27 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 5 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 95 _pdbx_nmr_constraints.NOE_constraints_total 567 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 ZUK B 2 ? ? 106.27 121.78 2 3 ZUK C 2 ? ? 105.99 -78.73 3 4 ZUK B 2 ? ? 89.49 91.21 4 5 ZUK B 2 ? ? 89.00 101.38 5 8 ZUK B 2 ? ? 105.53 93.26 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DAR N N N N 73 DAR CA C N R 74 DAR CB C N N 75 DAR CG C N N 76 DAR CD C N N 77 DAR NE N N N 78 DAR CZ C N N 79 DAR NH1 N N N 80 DAR NH2 N N N 81 DAR C C N N 82 DAR O O N N 83 DAR OXT O N N 84 DAR H H N N 85 DAR H2 H N N 86 DAR HA H N N 87 DAR HB2 H N N 88 DAR HB3 H N N 89 DAR HG2 H N N 90 DAR HG3 H N N 91 DAR HD2 H N N 92 DAR HD3 H N N 93 DAR HE H N N 94 DAR HH11 H N N 95 DAR HH12 H N N 96 DAR HH21 H N N 97 DAR HH22 H N N 98 DAR HXT H N N 99 G OP3 O N N 100 G P P N N 101 G OP1 O N N 102 G OP2 O N N 103 G "O5'" O N N 104 G "C5'" C N N 105 G "C4'" C N R 106 G "O4'" O N N 107 G "C3'" C N S 108 G "O3'" O N N 109 G "C2'" C N R 110 G "O2'" O N N 111 G "C1'" C N R 112 G N9 N Y N 113 G C8 C Y N 114 G N7 N Y N 115 G C5 C Y N 116 G C6 C N N 117 G O6 O N N 118 G N1 N N N 119 G C2 C N N 120 G N2 N N N 121 G N3 N N N 122 G C4 C Y N 123 G HOP3 H N N 124 G HOP2 H N N 125 G "H5'" H N N 126 G "H5''" H N N 127 G "H4'" H N N 128 G "H3'" H N N 129 G "HO3'" H N N 130 G "H2'" H N N 131 G "HO2'" H N N 132 G "H1'" H N N 133 G H8 H N N 134 G H1 H N N 135 G H21 H N N 136 G H22 H N N 137 NH2 N N N N 138 NH2 HN1 H N N 139 NH2 HN2 H N N 140 U OP3 O N N 141 U P P N N 142 U OP1 O N N 143 U OP2 O N N 144 U "O5'" O N N 145 U "C5'" C N N 146 U "C4'" C N R 147 U "O4'" O N N 148 U "C3'" C N S 149 U "O3'" O N N 150 U "C2'" C N R 151 U "O2'" O N N 152 U "C1'" C N R 153 U N1 N N N 154 U C2 C N N 155 U O2 O N N 156 U N3 N N N 157 U C4 C N N 158 U O4 O N N 159 U C5 C N N 160 U C6 C N N 161 U HOP3 H N N 162 U HOP2 H N N 163 U "H5'" H N N 164 U "H5''" H N N 165 U "H4'" H N N 166 U "H3'" H N N 167 U "HO3'" H N N 168 U "H2'" H N N 169 U "HO2'" H N N 170 U "H1'" H N N 171 U H3 H N N 172 U H5 H N N 173 U H6 H N N 174 ZUK C C N N 175 ZUK N N N N 176 ZUK O O N N 177 ZUK CA C N R 178 ZUK CB C N N 179 ZUK CD C N N 180 ZUK CE C Y N 181 ZUK CG C N N 182 ZUK CT C Y N 183 ZUK CH1 C Y N 184 ZUK CH2 C Y N 185 ZUK OXT O N N 186 ZUK NZ1 N Y N 187 ZUK NZ2 N Y N 188 ZUK H H N N 189 ZUK HA H N N 190 ZUK HT H N N 191 ZUK HB H N N 192 ZUK HD H N N 193 ZUK HG H N N 194 ZUK HBA H N N 195 ZUK HDA H N N 196 ZUK HGA H N N 197 ZUK HH1 H N N 198 ZUK HH2 H N N 199 ZUK H2 H N N 200 ZUK HXT H N N 201 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DAR N CA sing N N 76 DAR N H sing N N 77 DAR N H2 sing N N 78 DAR CA CB sing N N 79 DAR CA C sing N N 80 DAR CA HA sing N N 81 DAR CB CG sing N N 82 DAR CB HB2 sing N N 83 DAR CB HB3 sing N N 84 DAR CG CD sing N N 85 DAR CG HG2 sing N N 86 DAR CG HG3 sing N N 87 DAR CD NE sing N N 88 DAR CD HD2 sing N N 89 DAR CD HD3 sing N N 90 DAR NE CZ sing N N 91 DAR NE HE sing N N 92 DAR CZ NH1 sing N N 93 DAR CZ NH2 doub N N 94 DAR NH1 HH11 sing N N 95 DAR NH1 HH12 sing N N 96 DAR NH2 HH21 sing N N 97 DAR NH2 HH22 sing N N 98 DAR C O doub N N 99 DAR C OXT sing N N 100 DAR OXT HXT sing N N 101 G OP3 P sing N N 102 G OP3 HOP3 sing N N 103 G P OP1 doub N N 104 G P OP2 sing N N 105 G P "O5'" sing N N 106 G OP2 HOP2 sing N N 107 G "O5'" "C5'" sing N N 108 G "C5'" "C4'" sing N N 109 G "C5'" "H5'" sing N N 110 G "C5'" "H5''" sing N N 111 G "C4'" "O4'" sing N N 112 G "C4'" "C3'" sing N N 113 G "C4'" "H4'" sing N N 114 G "O4'" "C1'" sing N N 115 G "C3'" "O3'" sing N N 116 G "C3'" "C2'" sing N N 117 G "C3'" "H3'" sing N N 118 G "O3'" "HO3'" sing N N 119 G "C2'" "O2'" sing N N 120 G "C2'" "C1'" sing N N 121 G "C2'" "H2'" sing N N 122 G "O2'" "HO2'" sing N N 123 G "C1'" N9 sing N N 124 G "C1'" "H1'" sing N N 125 G N9 C8 sing Y N 126 G N9 C4 sing Y N 127 G C8 N7 doub Y N 128 G C8 H8 sing N N 129 G N7 C5 sing Y N 130 G C5 C6 sing N N 131 G C5 C4 doub Y N 132 G C6 O6 doub N N 133 G C6 N1 sing N N 134 G N1 C2 sing N N 135 G N1 H1 sing N N 136 G C2 N2 sing N N 137 G C2 N3 doub N N 138 G N2 H21 sing N N 139 G N2 H22 sing N N 140 G N3 C4 sing N N 141 NH2 N HN1 sing N N 142 NH2 N HN2 sing N N 143 U OP3 P sing N N 144 U OP3 HOP3 sing N N 145 U P OP1 doub N N 146 U P OP2 sing N N 147 U P "O5'" sing N N 148 U OP2 HOP2 sing N N 149 U "O5'" "C5'" sing N N 150 U "C5'" "C4'" sing N N 151 U "C5'" "H5'" sing N N 152 U "C5'" "H5''" sing N N 153 U "C4'" "O4'" sing N N 154 U "C4'" "C3'" sing N N 155 U "C4'" "H4'" sing N N 156 U "O4'" "C1'" sing N N 157 U "C3'" "O3'" sing N N 158 U "C3'" "C2'" sing N N 159 U "C3'" "H3'" sing N N 160 U "O3'" "HO3'" sing N N 161 U "C2'" "O2'" sing N N 162 U "C2'" "C1'" sing N N 163 U "C2'" "H2'" sing N N 164 U "O2'" "HO2'" sing N N 165 U "C1'" N1 sing N N 166 U "C1'" "H1'" sing N N 167 U N1 C2 sing N N 168 U N1 C6 sing N N 169 U C2 O2 doub N N 170 U C2 N3 sing N N 171 U N3 C4 sing N N 172 U N3 H3 sing N N 173 U C4 O4 doub N N 174 U C4 C5 sing N N 175 U C5 C6 doub N N 176 U C5 H5 sing N N 177 U C6 H6 sing N N 178 ZUK C CA sing N N 179 ZUK N H sing N N 180 ZUK N CA sing N N 181 ZUK N H2 sing N N 182 ZUK O C doub N N 183 ZUK CA HA sing N N 184 ZUK CA CB sing N N 185 ZUK CB HBA sing N N 186 ZUK CB CG sing N N 187 ZUK CD HDA sing N N 188 ZUK CD CE sing N N 189 ZUK CE NZ1 sing Y N 190 ZUK CG CD sing N N 191 ZUK CG HGA sing N N 192 ZUK CT CH1 sing Y N 193 ZUK CT HT sing N N 194 ZUK CH1 HH1 sing N N 195 ZUK CH2 CT doub Y N 196 ZUK OXT C sing N N 197 ZUK OXT HXT sing N N 198 ZUK NZ1 CH1 doub Y N 199 ZUK NZ2 CE doub Y N 200 ZUK NZ2 CH2 sing Y N 201 ZUK HB CB sing N N 202 ZUK HD CD sing N N 203 ZUK HG CG sing N N 204 ZUK HH2 CH2 sing N N 205 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KMJ 'double helix' 2KMJ 'a-form double helix' 2KMJ 'bulge loop' 2KMJ 'mismatched base pair' 2KMJ 'triple 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 28 1_555 0.020 -0.423 -1.426 7.485 -7.011 2.267 1 A_G16:C46_A A 16 ? A 46 ? 19 1 1 A G 2 1_555 A U 27 1_555 -2.113 -0.093 0.067 0.884 -2.018 6.433 2 A_G17:U45_A A 17 ? A 45 ? 28 1 1 A C 3 1_555 A G 26 1_555 1.058 -0.300 0.045 -1.462 -1.970 -4.718 3 A_C18:G44_A A 18 ? A 44 ? 19 1 1 A C 4 1_555 A G 25 1_555 0.921 -0.185 0.085 -1.171 -3.044 -0.994 4 A_C19:G43_A A 19 ? A 43 ? 19 1 1 A A 5 1_555 A U 24 1_555 0.064 -0.043 -0.207 -3.791 2.225 -6.039 5 A_A20:U42_A A 20 ? A 42 ? 20 1 1 A G 6 1_555 A C 23 1_555 0.398 0.156 -0.063 -2.182 -1.834 -3.095 6 A_G21:C41_A A 21 ? A 41 ? 19 1 1 A A 7 1_555 A U 22 1_555 -0.116 0.020 -0.187 2.927 5.197 -0.780 7 A_A22:U40_A A 22 ? A 40 ? 20 1 1 A G 10 1_555 A C 21 1_555 0.063 0.003 0.150 -1.100 -3.064 -0.484 8 A_G26:C39_A A 26 ? A 39 ? 19 1 1 A A 11 1_555 A U 20 1_555 -0.133 0.201 0.052 0.027 0.858 -8.174 9 A_A27:U38_A A 27 ? A 38 ? 20 1 1 A G 12 1_555 A C 19 1_555 0.379 0.155 -0.117 1.939 -2.532 -7.601 10 A_G28:C37_A A 28 ? A 37 ? 19 1 1 A C 13 1_555 A G 18 1_555 1.514 -0.702 -0.345 1.823 1.760 -8.084 11 A_C29:G36_A A 29 ? A 36 ? 19 1 1 A U 14 1_555 A G 17 1_555 0.467 -3.542 0.736 26.073 15.918 -124.634 12 A_U31:G34_A A 31 ? A 34 ? ? ? # 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 28 1_555 A G 2 1_555 A U 27 1_555 0.247 -1.697 3.632 -11.352 11.653 29.302 -4.894 -2.324 2.534 21.110 20.564 33.429 1 AA_G16G17:U45C46_AA A 16 ? A 46 ? A 17 ? A 45 ? 1 A G 2 1_555 A U 27 1_555 A C 3 1_555 A G 26 1_555 -0.236 -1.256 3.887 2.226 2.743 46.270 -1.867 0.521 3.796 3.484 -2.828 46.398 2 AA_G17C18:G44U45_AA A 17 ? A 45 ? A 18 ? A 44 ? 1 A C 3 1_555 A G 26 1_555 A C 4 1_555 A G 25 1_555 -0.122 -2.128 3.404 0.630 8.686 27.018 -6.230 0.385 2.603 18.007 -1.307 28.362 3 AA_C18C19:G43G44_AA A 18 ? A 44 ? A 19 ? A 43 ? 1 A C 4 1_555 A G 25 1_555 A A 5 1_555 A U 24 1_555 -0.855 -1.794 3.459 4.794 0.791 34.598 -3.113 2.175 3.274 1.321 -8.012 34.927 4 AA_C19A20:U42G43_AA A 19 ? A 43 ? A 20 ? A 42 ? 1 A A 5 1_555 A U 24 1_555 A G 6 1_555 A C 23 1_555 0.430 -1.951 3.567 1.463 -3.946 32.833 -2.674 -0.476 3.784 -6.945 -2.575 33.094 5 AA_A20G21:C41U42_AA A 20 ? A 42 ? A 21 ? A 41 ? 1 A G 6 1_555 A C 23 1_555 A A 7 1_555 A U 22 1_555 -0.606 -1.875 3.306 -0.140 6.309 28.001 -5.133 1.193 2.827 12.833 0.285 28.690 6 AA_G21A22:U40C41_AA A 21 ? A 41 ? A 22 ? A 40 ? 1 A A 7 1_555 A U 22 1_555 A G 10 1_555 A C 21 1_555 0.031 -2.841 4.048 5.016 -11.288 27.219 -2.201 1.414 4.759 -22.569 -10.030 29.842 7 AA_A22G26:C39U40_AA A 22 ? A 40 ? A 26 ? A 39 ? 1 A G 10 1_555 A C 21 1_555 A A 11 1_555 A U 20 1_555 -0.409 -2.039 3.604 2.436 -9.900 29.790 -1.543 1.300 4.014 -18.585 -4.572 31.449 8 AA_G26A27:U38C39_AA A 26 ? A 39 ? A 27 ? A 38 ? 1 A A 11 1_555 A U 20 1_555 A G 12 1_555 A C 19 1_555 0.140 -1.958 3.417 1.724 2.263 31.867 -3.972 0.065 3.276 4.112 -3.133 31.991 9 AA_A27G28:C37U38_AA A 27 ? A 38 ? A 28 ? A 37 ? 1 A G 12 1_555 A C 19 1_555 A C 13 1_555 A G 18 1_555 -0.949 -1.284 3.763 1.003 17.493 34.777 -4.202 1.558 2.799 27.234 -1.562 38.820 10 AA_G28C29:G36C37_AA A 28 ? A 37 ? A 29 ? A 36 ? 1 A C 13 1_555 A G 18 1_555 A U 14 1_555 A G 17 1_555 -2.390 -0.891 3.433 -0.967 13.177 90.563 -0.890 1.652 3.330 9.232 0.677 91.314 11 AA_C29U31:G34G36_AA A 29 ? A 36 ? A 31 ? A 34 ? #