data_1NK3 # _entry.id 1NK3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1NK3 pdb_00001nk3 10.2210/pdb1nk3/pdb WWPDB D_1000175317 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1NK2 _pdbx_database_related.details 'ENSEMBLE OF 20 STRUCTURES' _pdbx_database_related.content_type ensemble # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NK3 _pdbx_database_status.recvd_initial_deposition_date 1998-05-06 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Gruschus, J.M.' 1 'Tsao, D.H.H.' 2 'Wang, L.-H.' 3 'Nirenberg, M.' 4 'Ferretti, J.A.' 5 # 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 'Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.' Biochemistry 36 5372 5380 1997 BICHAW US 0006-2960 0033 ? 9154919 10.1021/bi9620060 1 'Interactions of the Vnd/Nk-2 Homeodomain with DNA by Nuclear Magnetic Resonance Spectroscopy: Basis of Binding Specificity' Biochemistry 36 5372 ? 1997 BICHAW US 0006-2960 0033 ? ? ? 2 'The Three-Dimensional Solution Structure of the Nk-2 Homeodomain from Drosophila' J.Mol.Biol. 251 297 ? 1995 JMOBAK UK 0022-2836 0070 ? ? ? 3 'Elongation of Helix III of the Nk-2 Homeodomain Upon Binding to DNA: A Secondary Structure Study by NMR' Biochemistry 33 15053 ? 1994 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gruschus, J.M.' 1 ? primary 'Tsao, D.H.' 2 ? primary 'Wang, L.H.' 3 ? primary 'Nirenberg, M.' 4 ? primary 'Ferretti, J.A.' 5 ? 1 'Gruschus, J.M.' 6 ? 1 'Tsao, D.H.' 7 ? 1 'Wang, L.H.' 8 ? 1 'Nirenberg, M.' 9 ? 1 'Ferretti, J.A.' 10 ? 2 'Tsao, D.H.' 11 ? 2 'Gruschus, J.M.' 12 ? 2 'Wang, L.H.' 13 ? 2 'Nirenberg, M.' 14 ? 2 'Ferretti, J.A.' 15 ? 3 'Tsao, D.H.' 16 ? 3 'Gruschus, J.M.' 17 ? 3 'Wang, L.H.' 18 ? 3 'Nirenberg, M.' 19 ? 3 'Ferretti, J.A.' 20 ? # _cell.entry_id 1NK3 _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 1NK3 _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 ;DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3') ; 4960.211 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3') ; 4836.171 1 ? ? ? ? 3 polymer man 'HOMEOBOX PROTEIN VND' 9374.741 1 ? ? HOMEODOMAIN ? # _entity_name_com.entity_id 3 _entity_name_com.name 'VND/NK-2 HOMEODOMAIN, VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN, HOMEOBOX PROTEIN NK-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 polydeoxyribonucleotide no no '(DT)(DG)(DT)(DG)(DT)(DC)(DA)(DA)(DG)(DT)(DG)(DG)(DC)(DT)(DG)(DT)' TGTGTCAAGTGGCTGT A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DA)(DG)(DC)(DC)(DA)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DC)(DA)' ACAGCCACTTGACACA B ? 3 'polypeptide(L)' no no ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP P ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DG n 1 3 DT n 1 4 DG n 1 5 DT n 1 6 DC n 1 7 DA n 1 8 DA n 1 9 DG n 1 10 DT n 1 11 DG n 1 12 DG n 1 13 DC n 1 14 DT n 1 15 DG n 1 16 DT n 2 1 DA n 2 2 DC n 2 3 DA n 2 4 DG n 2 5 DC n 2 6 DC n 2 7 DA n 2 8 DC n 2 9 DT n 2 10 DT n 2 11 DG n 2 12 DA n 2 13 DC n 2 14 DA n 2 15 DC n 2 16 DA n 3 1 ALA n 3 2 SER n 3 3 ASP n 3 4 GLY n 3 5 LEU n 3 6 PRO n 3 7 ASN n 3 8 LYS n 3 9 LYS n 3 10 ARG n 3 11 LYS n 3 12 ARG n 3 13 ARG n 3 14 VAL n 3 15 LEU n 3 16 PHE n 3 17 THR n 3 18 LYS n 3 19 ALA n 3 20 GLN n 3 21 THR n 3 22 TYR n 3 23 GLU n 3 24 LEU n 3 25 GLU n 3 26 ARG n 3 27 ARG n 3 28 PHE n 3 29 ARG n 3 30 GLN n 3 31 GLN n 3 32 ARG n 3 33 TYR n 3 34 LEU n 3 35 SER n 3 36 ALA n 3 37 PRO n 3 38 GLU n 3 39 ARG n 3 40 GLU n 3 41 HIS n 3 42 LEU n 3 43 ALA n 3 44 SER n 3 45 LEU n 3 46 ILE n 3 47 ARG n 3 48 LEU n 3 49 THR n 3 50 PRO n 3 51 THR n 3 52 GLN n 3 53 VAL n 3 54 LYS n 3 55 ILE n 3 56 TRP n 3 57 PHE n 3 58 GLN n 3 59 ASN n 3 60 HIS n 3 61 ARG n 3 62 TYR n 3 63 LYS n 3 64 THR n 3 65 LYS n 3 66 ARG n 3 67 ALA n 3 68 GLN n 3 69 ASN n 3 70 GLU n 3 71 LYS n 3 72 GLY n 3 73 TYR n 3 74 GLU n 3 75 GLY n 3 76 HIS n 3 77 PRO n # _entity_src_gen.entity_id 3 _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 'fruit fly' _entity_src_gen.gene_src_genus Drosophila _entity_src_gen.pdbx_gene_src_gene POTENTIAL _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 'Drosophila melanogaster' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 7227 _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 FRUIT _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 Escherichia _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PET11D _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP VND_DROME 3 ? ? P22808 ? 2 PDB 1NK3 1 ? ? 1NK3 ? 3 PDB 1NK3 2 ? ? 1NK3 ? # 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 1NK3 P 8 ? 70 ? P22808 68 ? 130 ? 100 162 2 2 1NK3 A 1 ? 16 ? 1NK3 1 ? 16 ? 1 16 3 3 1NK3 B 1 ? 16 ? 1NK3 17 ? 32 ? 17 32 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '15N-EDITED 3D NOESY H2O' 1 2 1 '13C-EDITED 3D NOESY D2O' 1 3 1 '12C-FILTERED 2D NOESY D2O' 1 4 1 '1-1 SEMISELECTIVE 2D NOESY H2O' 1 5 1 'DEUTERIUM EXCHANGE 15N 2D HMQC H2O' 1 6 1 'QUANTITATIVE HN-HALPHA J-COUPLING' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 308 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 60mM _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents H2O # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AMX600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1NK3 _pdbx_nmr_refine.method 'DISTANCE GEOMETRY/ SIMULATED ANNEALING' _pdbx_nmr_refine.details 'NMR REFINE/INSIGHT II 97' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1NK3 _pdbx_nmr_details.text ;THIS MODEL IS THE AVERAGE STRUCTURE OF THE ENSEMBLE OF 20 STRUCTURES (1NK2). THE UNSTRUCTURED N-TERMINAL AND C-TERMINAL AMINO ACIDS (P 101-P 107 AND P 171-P 177 IN PDB ENTRY 1NK2) WERE REMOVED PRIOR TO MINIMIZATION OF THE AVERAGE STRUCTURE BY THE MD_SCHE DULE PROGRAM OF INSIGHTII/NMR REFINE, SUBJECT TO ALL EXPERIMENTAL RESTRAINTS FOR THE DNA AND REMAINING PROTEIN RESIDUES. THE REMAINING PROTEIN RESIDUES ARE RENUMBERED STARTING WITH P 100 SO THAT THE RESIDUE NUMBERING FOLLOWS THE STANDARD, CANONICAL NUMBER ING SCHEME FOR HOMEODOMAINS. ; # _pdbx_nmr_ensemble.entry_id 1NK3 _pdbx_nmr_ensemble.conformers_calculated_total_number 80 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST RESTRAINT VIOLATION' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement 'INSIGHT II 97 AUTHOR : MSI' MSI ? 1 'structure solution' 'NMR REFINE' REFINE ? 2 # _exptl.entry_id 1NK3 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1NK3 _struct.title 'VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NK3 _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN/DNA' _struct_keywords.text 'HOMEODOMAIN, HOMEOBOX, DNA-BINDING PROTEIN, EMBRYONIC DEVELOPMENT, COMPLEX (HOMEODOMAIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 I LYS C 18 ? GLN C 30 ? LYS P 110 GLN P 122 1 ? 13 HELX_P HELX_P2 II ALA C 36 ? ILE C 46 ? ALA P 128 ILE P 138 1 ? 11 HELX_P HELX_P3 III PRO C 50 ? GLU C 70 ? PRO P 142 GLU P 162 1 ? 21 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 15 N3 ? ? A DG 2 B DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 15 O2 ? ? A DG 2 B DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 15 N4 ? ? A DG 2 B DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DA 16 N1 ? ? A DG 2 B DA 32 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DA 16 N6 ? ? A DG 2 B DA 32 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 14 N1 ? ? A DT 3 B DA 30 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 13 N3 ? ? A DG 4 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 13 O2 ? ? A DG 4 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 13 N4 ? ? A DG 4 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 6 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 6 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 6 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 7 B DT 25 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog14 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 7 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 7 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 8 B DT 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 8 B DT 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 10 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 10 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 11 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 11 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 11 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 12 B DC 21 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog27 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 12 B DC 22 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog28 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 13 B DG 20 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog29 hydrog ? ? A DT 14 O4 ? ? ? 1_555 B DC 2 N4 ? ? A DT 14 B DC 18 1_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog30 hydrog ? ? A DT 14 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 14 B DA 19 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1NK3 _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 1NK3 _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 DT 1 1 1 DT T A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DT 10 10 10 DT T A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DG 12 12 12 DG G A . n A 1 13 DC 13 13 13 DC C A . n A 1 14 DT 14 14 14 DT T A . n A 1 15 DG 15 15 15 DG G A . n A 1 16 DT 16 16 16 DT T A . n B 2 1 DA 1 17 17 DA A B . n B 2 2 DC 2 18 18 DC C B . n B 2 3 DA 3 19 19 DA A B . n B 2 4 DG 4 20 20 DG G B . n B 2 5 DC 5 21 21 DC C B . n B 2 6 DC 6 22 22 DC C B . n B 2 7 DA 7 23 23 DA A B . n B 2 8 DC 8 24 24 DC C B . n B 2 9 DT 9 25 25 DT T B . n B 2 10 DT 10 26 26 DT T B . n B 2 11 DG 11 27 27 DG G B . n B 2 12 DA 12 28 28 DA A B . n B 2 13 DC 13 29 29 DC C B . n B 2 14 DA 14 30 30 DA A B . n B 2 15 DC 15 31 31 DC C B . n B 2 16 DA 16 32 32 DA A B . n C 3 1 ALA 1 93 ? ? ? P . n C 3 2 SER 2 94 ? ? ? P . n C 3 3 ASP 3 95 ? ? ? P . n C 3 4 GLY 4 96 ? ? ? P . n C 3 5 LEU 5 97 ? ? ? P . n C 3 6 PRO 6 98 ? ? ? P . n C 3 7 ASN 7 99 ? ? ? P . n C 3 8 LYS 8 100 100 LYS LYS P . n C 3 9 LYS 9 101 101 LYS LYS P . n C 3 10 ARG 10 102 102 ARG ARG P . n C 3 11 LYS 11 103 103 LYS LYS P . n C 3 12 ARG 12 104 104 ARG ARG P . n C 3 13 ARG 13 105 105 ARG ARG P . n C 3 14 VAL 14 106 106 VAL VAL P . n C 3 15 LEU 15 107 107 LEU LEU P . n C 3 16 PHE 16 108 108 PHE PHE P . n C 3 17 THR 17 109 109 THR THR P . n C 3 18 LYS 18 110 110 LYS LYS P . n C 3 19 ALA 19 111 111 ALA ALA P . n C 3 20 GLN 20 112 112 GLN GLN P . n C 3 21 THR 21 113 113 THR THR P . n C 3 22 TYR 22 114 114 TYR TYR P . n C 3 23 GLU 23 115 115 GLU GLU P . n C 3 24 LEU 24 116 116 LEU LEU P . n C 3 25 GLU 25 117 117 GLU GLU P . n C 3 26 ARG 26 118 118 ARG ARG P . n C 3 27 ARG 27 119 119 ARG ARG P . n C 3 28 PHE 28 120 120 PHE PHE P . n C 3 29 ARG 29 121 121 ARG ARG P . n C 3 30 GLN 30 122 122 GLN GLN P . n C 3 31 GLN 31 123 123 GLN GLN P . n C 3 32 ARG 32 124 124 ARG ARG P . n C 3 33 TYR 33 125 125 TYR TYR P . n C 3 34 LEU 34 126 126 LEU LEU P . n C 3 35 SER 35 127 127 SER SER P . n C 3 36 ALA 36 128 128 ALA ALA P . n C 3 37 PRO 37 129 129 PRO PRO P . n C 3 38 GLU 38 130 130 GLU GLU P . n C 3 39 ARG 39 131 131 ARG ARG P . n C 3 40 GLU 40 132 132 GLU GLU P . n C 3 41 HIS 41 133 133 HIS HIS P . n C 3 42 LEU 42 134 134 LEU LEU P . n C 3 43 ALA 43 135 135 ALA ALA P . n C 3 44 SER 44 136 136 SER SER P . n C 3 45 LEU 45 137 137 LEU LEU P . n C 3 46 ILE 46 138 138 ILE ILE P . n C 3 47 ARG 47 139 139 ARG ARG P . n C 3 48 LEU 48 140 140 LEU LEU P . n C 3 49 THR 49 141 141 THR THR P . n C 3 50 PRO 50 142 142 PRO PRO P . n C 3 51 THR 51 143 143 THR THR P . n C 3 52 GLN 52 144 144 GLN GLN P . n C 3 53 VAL 53 145 145 VAL VAL P . n C 3 54 LYS 54 146 146 LYS LYS P . n C 3 55 ILE 55 147 147 ILE ILE P . n C 3 56 TRP 56 148 148 TRP TRP P . n C 3 57 PHE 57 149 149 PHE PHE P . n C 3 58 GLN 58 150 150 GLN GLN P . n C 3 59 ASN 59 151 151 ASN ASN P . n C 3 60 HIS 60 152 152 HIS HIS P . n C 3 61 ARG 61 153 153 ARG ARG P . n C 3 62 TYR 62 154 154 TYR TYR P . n C 3 63 LYS 63 155 155 LYS LYS P . n C 3 64 THR 64 156 156 THR THR P . n C 3 65 LYS 65 157 157 LYS LYS P . n C 3 66 ARG 66 158 158 ARG ARG P . n C 3 67 ALA 67 159 159 ALA ALA P . n C 3 68 GLN 68 160 160 GLN GLN P . n C 3 69 ASN 69 161 161 ASN ASN P . n C 3 70 GLU 70 162 162 GLU GLU P . n C 3 71 LYS 71 163 ? ? ? P . n C 3 72 GLY 72 164 ? ? ? P . n C 3 73 TYR 73 165 ? ? ? P . n C 3 74 GLU 74 166 ? ? ? P . n C 3 75 GLY 75 167 ? ? ? P . n C 3 76 HIS 76 168 ? ? ? P . n C 3 77 PRO 77 169 ? ? ? P . 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 1998-12-09 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other # 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 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' # 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 "H2'" A DG 15 ? ? H71 A DT 16 ? ? 1.05 2 1 "H2''" B DC 24 ? ? "H5''" B DT 25 ? ? 1.29 # 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 1 "C2'" A DT 1 ? ? "C1'" A DT 1 ? ? 1.579 1.519 0.060 0.010 N 2 1 C6 A DG 9 ? ? N1 A DG 9 ? ? 1.437 1.391 0.046 0.007 N 3 1 C6 A DG 11 ? ? N1 A DG 11 ? ? 1.437 1.391 0.046 0.007 N 4 1 C4 A DC 13 ? ? C5 A DC 13 ? ? 1.474 1.425 0.049 0.008 N 5 1 C6 A DG 15 ? ? N1 A DG 15 ? ? 1.433 1.391 0.042 0.007 N 6 1 C4 B DC 18 ? ? C5 B DC 18 ? ? 1.474 1.425 0.049 0.008 N 7 1 "O3'" B DA 32 ? ? "C3'" B DA 32 ? ? 1.381 1.419 -0.038 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 1 ? ? "C4'" A DT 1 ? ? "C3'" A DT 1 ? ? 101.90 104.50 -2.60 0.40 N 2 1 "C3'" A DT 1 ? ? "O3'" A DT 1 ? ? P A DG 2 ? ? 130.49 119.70 10.79 1.20 Y 3 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 107.56 111.50 -3.94 0.50 N 4 1 N1 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 124.70 119.90 4.80 0.60 N 5 1 P A DT 3 ? ? "O5'" A DT 3 ? ? "C5'" A DT 3 ? ? 103.98 120.90 -16.92 1.60 N 6 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 107.13 111.50 -4.37 0.50 N 7 1 C6 A DG 4 ? ? C5 A DG 4 ? ? N7 A DG 4 ? ? 126.75 130.40 -3.65 0.60 N 8 1 N1 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 125.67 119.90 5.77 0.60 N 9 1 N3 A DT 5 ? ? C4 A DT 5 ? ? O4 A DT 5 ? ? 123.59 119.90 3.69 0.60 N 10 1 C4 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 114.87 119.00 -4.13 0.60 N 11 1 C2 A DC 6 ? ? N3 A DC 6 ? ? C4 A DC 6 ? ? 123.05 119.90 3.15 0.50 N 12 1 P A DA 8 ? ? "O5'" A DA 8 ? ? "C5'" A DA 8 ? ? 108.57 120.90 -12.33 1.60 N 13 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 111.15 108.30 2.85 0.30 N 14 1 C6 A DA 8 ? ? N1 A DA 8 ? ? C2 A DA 8 ? ? 122.74 118.60 4.14 0.60 N 15 1 C2 A DA 8 ? ? N3 A DA 8 ? ? C4 A DA 8 ? ? 107.55 110.60 -3.05 0.50 N 16 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 128.97 123.70 5.27 0.80 N 17 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.45 108.30 2.15 0.30 N 18 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 107.15 111.50 -4.35 0.50 N 19 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 125.46 119.90 5.56 0.60 N 20 1 C8 A DG 9 ? ? N9 A DG 9 ? ? "C1'" A DG 9 ? ? 135.52 127.00 8.52 1.30 N 21 1 C4 A DG 9 ? ? N9 A DG 9 ? ? "C1'" A DG 9 ? ? 118.55 126.50 -7.95 1.30 N 22 1 C5 A DG 11 ? ? C6 A DG 11 ? ? N1 A DG 11 ? ? 108.45 111.50 -3.05 0.50 N 23 1 N1 A DG 11 ? ? C6 A DG 11 ? ? O6 A DG 11 ? ? 124.10 119.90 4.20 0.60 N 24 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.28 108.30 1.98 0.30 N 25 1 C5 A DG 12 ? ? C6 A DG 12 ? ? N1 A DG 12 ? ? 106.63 111.50 -4.87 0.50 N 26 1 N1 A DG 12 ? ? C6 A DG 12 ? ? O6 A DG 12 ? ? 124.70 119.90 4.80 0.60 N 27 1 C4 A DC 13 ? ? C5 A DC 13 ? ? C6 A DC 13 ? ? 113.99 117.40 -3.41 0.50 N 28 1 "O4'" A DG 15 ? ? "C1'" A DG 15 ? ? N9 A DG 15 ? ? 101.41 108.00 -6.59 0.70 N 29 1 C5 A DG 15 ? ? C6 A DG 15 ? ? N1 A DG 15 ? ? 107.06 111.50 -4.44 0.50 N 30 1 N1 A DG 15 ? ? C6 A DG 15 ? ? O6 A DG 15 ? ? 124.16 119.90 4.26 0.60 N 31 1 "O4'" A DT 16 ? ? "C4'" A DT 16 ? ? "C3'" A DT 16 ? ? 100.16 104.50 -4.34 0.40 N 32 1 C4 A DT 16 ? ? C5 A DT 16 ? ? C7 A DT 16 ? ? 115.25 119.00 -3.75 0.60 N 33 1 C6 A DT 16 ? ? C5 A DT 16 ? ? C7 A DT 16 ? ? 126.75 122.90 3.85 0.60 N 34 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 102.95 108.00 -5.05 0.70 N 35 1 "C3'" B DA 17 ? ? "O3'" B DA 17 ? ? P B DC 18 ? ? 127.47 119.70 7.77 1.20 Y 36 1 "O4'" B DA 19 ? ? "C1'" B DA 19 ? ? N9 B DA 19 ? ? 110.22 108.30 1.92 0.30 N 37 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 110.12 108.30 1.82 0.30 N 38 1 C5 B DG 20 ? ? C6 B DG 20 ? ? N1 B DG 20 ? ? 107.02 111.50 -4.48 0.50 N 39 1 N1 B DG 20 ? ? C6 B DG 20 ? ? O6 B DG 20 ? ? 123.85 119.90 3.95 0.60 N 40 1 C2 B DC 21 ? ? N3 B DC 21 ? ? C4 B DC 21 ? ? 122.94 119.90 3.04 0.50 N 41 1 "C3'" B DC 21 ? ? "O3'" B DC 21 ? ? P B DC 22 ? ? 128.34 119.70 8.64 1.20 Y 42 1 "O4'" B DA 23 ? ? "C1'" B DA 23 ? ? N9 B DA 23 ? ? 111.68 108.30 3.38 0.30 N 43 1 C6 B DA 23 ? ? N1 B DA 23 ? ? C2 B DA 23 ? ? 122.27 118.60 3.67 0.60 N 44 1 C6 B DC 24 ? ? N1 B DC 24 ? ? C2 B DC 24 ? ? 122.95 120.30 2.65 0.40 N 45 1 C2 B DC 24 ? ? N1 B DC 24 ? ? "C1'" B DC 24 ? ? 110.84 118.80 -7.96 1.10 N 46 1 N3 B DT 25 ? ? C4 B DT 25 ? ? O4 B DT 25 ? ? 123.72 119.90 3.82 0.60 N 47 1 N3 B DT 26 ? ? C4 B DT 26 ? ? O4 B DT 26 ? ? 123.51 119.90 3.61 0.60 N 48 1 C4 B DT 26 ? ? C5 B DT 26 ? ? C7 B DT 26 ? ? 113.53 119.00 -5.47 0.60 N 49 1 C6 B DT 26 ? ? C5 B DT 26 ? ? C7 B DT 26 ? ? 127.81 122.90 4.91 0.60 N 50 1 C5 B DG 27 ? ? C6 B DG 27 ? ? N1 B DG 27 ? ? 107.74 111.50 -3.76 0.50 N 51 1 C6 B DG 27 ? ? C5 B DG 27 ? ? N7 B DG 27 ? ? 126.06 130.40 -4.34 0.60 N 52 1 N1 B DG 27 ? ? C6 B DG 27 ? ? O6 B DG 27 ? ? 126.16 119.90 6.26 0.60 N 53 1 "O4'" B DA 28 ? ? "C1'" B DA 28 ? ? N9 B DA 28 ? ? 112.13 108.30 3.83 0.30 N 54 1 C2 B DC 29 ? ? N1 B DC 29 ? ? "C1'" B DC 29 ? ? 111.73 118.80 -7.07 1.10 N 55 1 "O4'" B DA 30 ? ? "C1'" B DA 30 ? ? N9 B DA 30 ? ? 111.93 108.30 3.63 0.30 N 56 1 NE P ARG 119 ? ? CZ P ARG 119 ? ? NH1 P ARG 119 ? ? 123.74 120.30 3.44 0.50 N 57 1 N P GLN 123 ? ? CA P GLN 123 ? ? CB P GLN 123 ? ? 98.74 110.60 -11.86 1.80 N 58 1 NE P ARG 124 ? ? CZ P ARG 124 ? ? NH1 P ARG 124 ? ? 123.93 120.30 3.63 0.50 N 59 1 NE P ARG 131 ? ? CZ P ARG 131 ? ? NH1 P ARG 131 ? ? 123.37 120.30 3.07 0.50 N 60 1 CA P GLU 132 ? ? CB P GLU 132 ? ? CG P GLU 132 ? ? 127.19 113.40 13.79 2.20 N 61 1 NE P ARG 153 ? ? CZ P ARG 153 ? ? NH1 P ARG 153 ? ? 123.78 120.30 3.48 0.50 N 62 1 CB P LYS 155 ? ? CA P LYS 155 ? ? C P LYS 155 ? ? 98.38 110.40 -12.02 2.00 N 63 1 CA P LYS 155 ? ? CB P LYS 155 ? ? CG P LYS 155 ? ? 127.42 113.40 14.02 2.20 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 ARG P 102 ? ? -92.36 51.16 2 1 LYS P 103 ? ? 31.84 66.82 3 1 ARG P 139 ? ? 85.47 22.87 # 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 DG A 4 ? ? 0.057 'SIDE CHAIN' 2 1 DG A 9 ? ? 0.057 'SIDE CHAIN' 3 1 DT B 26 ? ? 0.115 'SIDE CHAIN' 4 1 DA B 28 ? ? 0.092 'SIDE CHAIN' 5 1 PHE P 149 ? ? 0.085 'SIDE CHAIN' # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 P ALA 93 ? C ALA 1 2 1 Y 1 P SER 94 ? C SER 2 3 1 Y 1 P ASP 95 ? C ASP 3 4 1 Y 1 P GLY 96 ? C GLY 4 5 1 Y 1 P LEU 97 ? C LEU 5 6 1 Y 1 P PRO 98 ? C PRO 6 7 1 Y 1 P ASN 99 ? C ASN 7 8 1 Y 1 P LYS 163 ? C LYS 71 9 1 Y 1 P GLY 164 ? C GLY 72 10 1 Y 1 P TYR 165 ? C TYR 73 11 1 Y 1 P GLU 166 ? C GLU 74 12 1 Y 1 P GLY 167 ? C GLY 75 13 1 Y 1 P HIS 168 ? C HIS 76 14 1 Y 1 P PRO 169 ? C PRO 77 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NK3 'double helix' 1NK3 'b-form double helix' 1NK3 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 2 1_555 B DC 15 1_555 0.024 -0.357 -1.621 2.031 1.547 -5.692 1 A_DG2:DC31_B A 2 ? B 31 ? 19 1 1 A DT 3 1_555 B DA 14 1_555 -1.003 0.356 -0.658 16.079 4.882 1.458 2 A_DT3:DA30_B A 3 ? B 30 ? ? ? 1 A DG 4 1_555 B DC 13 1_555 0.290 -0.204 -1.728 -23.597 -22.370 8.193 3 A_DG4:DC29_B A 4 ? B 29 ? 19 1 1 A DC 6 1_555 B DG 11 1_555 -0.001 -0.195 -1.332 23.114 -37.584 8.803 4 A_DC6:DG27_B A 6 ? B 27 ? 19 1 1 A DA 7 1_555 B DT 10 1_555 1.229 0.238 -0.367 -5.241 -23.141 2.902 5 A_DA7:DT26_B A 7 ? B 26 ? 20 1 1 A DA 8 1_555 B DT 9 1_555 0.492 0.048 0.652 18.021 -12.861 1.679 6 A_DA8:DT25_B A 8 ? B 25 ? 20 1 1 A DG 9 1_555 B DC 8 1_555 0.055 -0.198 1.034 12.386 -18.569 -15.841 7 A_DG9:DC24_B A 9 ? B 24 ? 19 1 1 A DT 10 1_555 B DA 7 1_555 -0.817 0.083 0.455 -0.290 -16.010 3.547 8 A_DT10:DA23_B A 10 ? B 23 ? 20 1 1 A DG 11 1_555 B DC 6 1_555 0.873 0.040 -1.452 -20.279 -25.158 5.668 9 A_DG11:DC22_B A 11 ? B 22 ? 19 1 1 A DG 12 1_555 B DC 5 1_555 0.930 -0.199 -2.136 -24.918 -6.928 -8.609 10 A_DG12:DC21_B A 12 ? B 21 ? ? ? 1 A DC 13 1_555 B DG 4 1_555 -0.950 -0.195 2.184 -31.393 18.825 0.244 11 A_DC13:DG20_B A 13 ? B 20 ? ? 1 1 A DT 14 1_555 B DC 2 1_555 -0.022 -0.121 -1.048 21.276 16.766 -26.559 12 A_DT14:DC18_B A 14 ? B 18 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 2 1_555 B DC 15 1_555 A DT 3 1_555 B DA 14 1_555 0.189 -0.179 3.374 -3.618 -7.897 33.063 0.990 -0.916 3.290 -13.587 6.224 34.155 1 AA_DG2DT3:DA30DC31_BB A 2 ? B 31 ? A 3 ? B 30 ? 1 A DT 3 1_555 B DA 14 1_555 A DG 4 1_555 B DC 13 1_555 0.852 2.404 4.501 9.055 6.947 51.599 2.054 -0.110 4.840 7.871 -10.260 52.762 2 AA_DT3DG4:DC29DA30_BB A 3 ? B 30 ? A 4 ? B 29 ? 1 A DG 4 1_555 B DC 13 1_555 A DC 6 1_555 B DG 11 1_555 -0.438 2.153 4.212 -8.352 12.699 69.409 1.262 -0.014 4.520 11.019 7.247 70.850 3 AA_DG4DC6:DG27DC29_BB A 4 ? B 29 ? A 6 ? B 27 ? 1 A DC 6 1_555 B DG 11 1_555 A DA 7 1_555 B DT 10 1_555 0.098 1.565 3.737 0.481 17.036 39.374 0.023 -0.074 4.053 23.968 -0.677 42.770 4 AA_DC6DA7:DT26DG27_BB A 6 ? B 27 ? A 7 ? B 26 ? 1 A DA 7 1_555 B DT 10 1_555 A DA 8 1_555 B DT 9 1_555 0.365 -0.164 2.335 -6.170 -5.860 32.969 0.382 -1.321 2.228 -10.117 10.652 34.020 5 AA_DA7DA8:DT25DT26_BB A 7 ? B 26 ? A 8 ? B 25 ? 1 A DA 8 1_555 B DT 9 1_555 A DG 9 1_555 B DC 8 1_555 -0.375 -0.994 3.101 -4.568 -2.051 29.854 -1.503 -0.176 3.181 -3.945 8.788 30.261 6 AA_DA8DG9:DC24DT25_BB A 8 ? B 25 ? A 9 ? B 24 ? 1 A DG 9 1_555 B DC 8 1_555 A DT 10 1_555 B DA 7 1_555 1.365 -1.179 3.687 4.513 1.623 38.369 -2.010 -1.428 3.766 2.457 -6.834 38.656 7 AA_DG9DT10:DA23DC24_BB A 9 ? B 24 ? A 10 ? B 23 ? 1 A DT 10 1_555 B DA 7 1_555 A DG 11 1_555 B DC 6 1_555 -0.053 1.097 3.754 12.414 16.087 38.565 -0.422 1.541 3.728 22.553 -17.404 43.410 8 AA_DT10DG11:DC22DA23_BB A 10 ? B 23 ? A 11 ? B 22 ? 1 A DG 11 1_555 B DC 6 1_555 A DG 12 1_555 B DC 5 1_555 -0.918 1.061 3.362 -1.872 10.405 32.708 0.027 1.237 3.569 17.902 3.221 34.330 9 AA_DG11DG12:DC21DC22_BB A 11 ? B 22 ? A 12 ? B 21 ? 1 A DG 12 1_555 B DC 5 1_555 A DC 13 1_555 B DG 4 1_555 0.731 0.824 4.647 -24.523 -11.637 33.690 2.664 -4.243 3.052 -17.061 35.954 43.016 10 AA_DG12DC13:DG20DC21_BB A 12 ? B 21 ? A 13 ? B 20 ? 1 A DC 13 1_555 B DG 4 1_555 A DT 14 1_555 B DC 2 1_555 -0.800 -0.684 3.899 -4.519 -7.807 40.890 0.043 0.541 4.020 -11.013 6.375 41.832 11 AA_DC13DT14:DC18DG20_BB A 13 ? B 20 ? A 14 ? B 18 ? #