data_1PDT # _entry.id 1PDT # _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 1PDT pdb_00001pdt 10.2210/pdb1pdt/pdb WWPDB D_1000175619 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1PDT _pdbx_database_status.recvd_initial_deposition_date 1996-03-28 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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 'Eriksson, M.' 1 'Nielsen, P.E.' 2 # 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 'Solution structure of a peptide nucleic acid-DNA duplex.' Nat.Struct.Biol. 3 410 413 1996 NSBIEW US 1072-8368 2024 ? 8612069 10.1038/nsb0596-410 1 'Structural Characterization of Pna-DNA Duplexes by NMR. Evidence for DNA in a B-Like Conformation' Biochemistry 33 9820 ? 1994 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Eriksson, M.' 1 ? primary 'Nielsen, P.E.' 2 ? 1 'Leijon, M.' 3 ? 1 'Graslund, A.' 4 ? 1 'Nielsen, P.E.' 5 ? 1 'Buchardt, O.' 6 ? 1 'Norden, B.' 7 ? 1 'Kristensen, S.M.' 8 ? 1 'Eriksson, M.' 9 ? # _cell.entry_id 1PDT _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 1PDT _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(*GP*AP*CP*AP*TP*AP*GP*C)-3' ; 2435.631 1 ? ? ? ? 2 polymer syn 'PEPTIDE NUCLEIC ACID (COOH-P(*G*C*T*A*T*G*T*C)-NH2)' 2120.155 1 ? ? ? 'PNA-DNA DUPLEX' # _entity_name_com.entity_id 2 _entity_name_com.name PNA # 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 '(DG)(DA)(DC)(DA)(DT)(DA)(DG)(DC)' GACATAGC A ? 2 polydeoxyribonucleotide no yes '(GPN)(CPN)(TPN)(APN)(TPN)(GPN)(TPN)(CPN)(NH2)' XXXXXXXXX B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DA n 1 3 DC n 1 4 DA n 1 5 DT n 1 6 DA n 1 7 DG n 1 8 DC n 2 1 GPN n 2 2 CPN n 2 3 TPN n 2 4 APN n 2 5 TPN n 2 6 GPN n 2 7 TPN n 2 8 CPN n 2 9 NH2 n # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1PDT 1PDT ? ? ? 2 2 PDB 1PDT 1PDT ? ? ? # 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 1PDT A 1 ? 8 ? 1PDT 1 ? 8 ? 1 8 2 2 1PDT B 1 ? 9 ? 1PDT 9 ? 17 ? 9 17 # 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 APN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE ? 'C11 H16 N7 O3 1' 294.290 CPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE ? 'C10 H16 N5 O4 1' 270.265 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 GPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE ? 'C11 H16 N7 O4 1' 310.289 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 TPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE ? 'C11 H17 N4 O5 1' 285.276 # _pdbx_nmr_ensemble.entry_id 1PDT _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version 3.1 _pdbx_nmr_software.authors BRUNGER _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 1PDT _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1PDT _struct.title 'PD235, PNA-DNA DUPLEX, NMR, 8 STRUCTURES' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PDT _struct_keywords.pdbx_keywords 'PEPTIDE NUCLEIC ACID/DNA' _struct_keywords.text 'COMPLEX (PEPTIDE NUCLEIC ACID-DNA), NUCLEIC ACID COMPLEX, DUPLEX, HYBRID, PEPTIDE NUCLEIC ACID-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 ? # _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 _struct_conn.pdbx_role covale1 covale both ? B GPN 1 C ? ? ? 1_555 B CPN 2 N ? ? B GPN 9 B CPN 10 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale2 covale both ? B CPN 2 C ? ? ? 1_555 B TPN 3 N ? ? B CPN 10 B TPN 11 1_555 ? ? ? ? ? ? ? 1.310 ? ? covale3 covale both ? B TPN 3 C ? ? ? 1_555 B APN 4 N ? ? B TPN 11 B APN 12 1_555 ? ? ? ? ? ? ? 1.310 ? ? covale4 covale both ? B APN 4 C ? ? ? 1_555 B TPN 5 N ? ? B APN 12 B TPN 13 1_555 ? ? ? ? ? ? ? 1.307 ? ? covale5 covale both ? B TPN 5 C ? ? ? 1_555 B GPN 6 N ? ? B TPN 13 B GPN 14 1_555 ? ? ? ? ? ? ? 1.307 ? ? covale6 covale both ? B GPN 6 C ? ? ? 1_555 B TPN 7 N ? ? B GPN 14 B TPN 15 1_555 ? ? ? ? ? ? ? 1.307 ? ? covale7 covale both ? B TPN 7 C ? ? ? 1_555 B CPN 8 N ? ? B TPN 15 B CPN 16 1_555 ? ? ? ? ? ? ? 1.310 ? ? covale8 covale both ? B CPN 8 C ? ? ? 1_555 B NH2 9 N ? ? B CPN 16 B NH2 17 1_555 ? ? ? ? ? ? ? 1.304 ? ? covale9 covale one ? B CPN 8 O ? ? ? 1_555 B NH2 9 N ? ? B CPN 16 B NH2 17 1_555 ? ? ? ? ? ? ? 1.092 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B CPN 8 N3 ? ? A DG 1 B CPN 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B CPN 8 O2 ? ? A DG 1 B CPN 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B CPN 8 N4 ? ? A DG 1 B CPN 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B TPN 7 N3 ? ? A DA 2 B TPN 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B TPN 7 O4 ? ? A DA 2 B TPN 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B GPN 6 N1 ? ? A DC 3 B GPN 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B GPN 6 O6 ? ? A DC 3 B GPN 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B GPN 6 N2 ? ? A DC 3 B GPN 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B TPN 5 N3 ? ? A DA 4 B TPN 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B TPN 5 O4 ? ? A DA 4 B TPN 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B APN 4 N1 ? ? A DT 5 B APN 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B APN 4 N6 ? ? A DT 5 B APN 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B TPN 3 N3 ? ? A DA 6 B TPN 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B TPN 3 O4 ? ? A DA 6 B TPN 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B CPN 2 N3 ? ? A DG 7 B CPN 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B CPN 2 O2 ? ? A DG 7 B CPN 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B CPN 2 N4 ? ? A DG 7 B CPN 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B GPN 1 N1 ? ? A DC 8 B GPN 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B GPN 1 O6 ? ? A DC 8 B GPN 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B GPN 1 N2 ? ? A DC 8 B GPN 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id NH2 _struct_site.pdbx_auth_seq_id 17 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE NH2 B 17' # 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 2 DC A 3 ? DC A 3 . ? 1_555 ? 2 AC1 2 CPN B 8 ? CPN B 16 . ? 1_555 ? # _database_PDB_matrix.entry_id 1PDT _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 1PDT _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 DG 1 1 1 DG G A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n B 2 1 GPN 1 9 9 GPN GPN B . n B 2 2 CPN 2 10 10 CPN CPN B . n B 2 3 TPN 3 11 11 TPN TPN B . n B 2 4 APN 4 12 12 APN APN B . n B 2 5 TPN 5 13 13 TPN TPN B . n B 2 6 GPN 6 14 14 GPN GPN B . n B 2 7 TPN 7 15 15 TPN TPN B . n B 2 8 CPN 8 16 16 CPN CPN B . n B 2 9 NH2 9 17 17 NH2 NH2 B . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 B GPN 1 B GPN 9 ? DG ? 2 B CPN 2 B CPN 10 ? DC ? 3 B TPN 3 B TPN 11 ? DT ? 4 B APN 4 B APN 12 ? DA ? 5 B TPN 5 B TPN 13 ? DT ? 6 B GPN 6 B GPN 14 ? DG ? 7 B TPN 7 B TPN 15 ? DT ? 8 B CPN 8 B CPN 16 ? DC ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1996-10-14 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Atomic model' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 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' atom_site 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_database_status 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site # 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' '_atom_site.B_iso_or_equiv' 2 4 'Structure model' '_atom_site.Cartn_x' 3 4 'Structure model' '_atom_site.Cartn_y' 4 4 'Structure model' '_atom_site.Cartn_z' 5 4 'Structure model' '_atom_site.auth_atom_id' 6 4 'Structure model' '_atom_site.label_atom_id' 7 4 'Structure model' '_database_2.pdbx_DOI' 8 4 'Structure model' '_database_2.pdbx_database_accession' 9 4 'Structure model' '_pdbx_database_status.process_site' 10 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 11 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 13 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # 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 "O4'" A DC 3 ? ? HN1 B NH2 17 ? ? 1.54 2 3 "O4'" A DC 3 ? ? HN1 B NH2 17 ? ? 1.54 3 5 "O4'" A DC 3 ? ? HN2 B NH2 17 ? ? 1.51 4 7 "O4'" A DC 3 ? ? HN2 B NH2 17 ? ? 1.52 # 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.36 108.30 3.06 0.30 N 2 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.18 108.30 2.88 0.30 N 3 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.77 108.30 2.47 0.30 N 4 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.18 108.30 3.88 0.30 N 5 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.99 108.30 2.69 0.30 N 6 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.88 122.90 -4.02 0.60 N 7 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.37 108.30 3.07 0.30 N 8 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.31 108.30 2.01 0.30 N 9 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.66 108.30 2.36 0.30 N 10 2 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.54 108.30 3.24 0.30 N 11 2 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.00 108.30 2.70 0.30 N 12 2 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.81 108.30 2.51 0.30 N 13 2 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.98 108.30 3.68 0.30 N 14 2 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.92 108.30 3.62 0.30 N 15 2 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.89 122.90 -4.01 0.60 N 16 2 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.31 108.30 3.01 0.30 N 17 2 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.80 108.30 3.50 0.30 N 18 2 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.38 108.30 2.08 0.30 N 19 3 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.36 108.30 3.06 0.30 N 20 3 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.11 108.30 2.81 0.30 N 21 3 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.75 108.30 2.45 0.30 N 22 3 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.23 108.30 3.93 0.30 N 23 3 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.20 108.30 2.90 0.30 N 24 3 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.91 122.90 -3.99 0.60 N 25 3 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.48 108.30 3.18 0.30 N 26 3 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.25 108.30 1.95 0.30 N 27 3 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 111.26 108.30 2.96 0.30 N 28 4 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.38 108.30 3.08 0.30 N 29 4 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.13 108.30 2.83 0.30 N 30 4 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.68 108.30 2.38 0.30 N 31 4 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.83 108.30 3.53 0.30 N 32 4 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.92 108.30 3.62 0.30 N 33 4 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.92 122.90 -3.98 0.60 N 34 4 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.17 108.30 2.87 0.30 N 35 4 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.74 108.30 3.44 0.30 N 36 4 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.27 108.30 1.97 0.30 N 37 5 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.41 108.30 3.11 0.30 N 38 5 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.25 108.30 2.95 0.30 N 39 5 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.76 108.30 2.46 0.30 N 40 5 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.23 108.30 3.93 0.30 N 41 5 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.17 108.30 2.87 0.30 N 42 5 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 119.00 122.90 -3.90 0.60 N 43 5 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.39 108.30 3.09 0.30 N 44 5 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.33 108.30 2.03 0.30 N 45 5 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 111.35 108.30 3.05 0.30 N 46 6 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.52 108.30 3.22 0.30 N 47 6 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 110.91 108.30 2.61 0.30 N 48 6 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.97 108.30 2.67 0.30 N 49 6 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.01 108.30 3.71 0.30 N 50 6 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 112.01 108.30 3.71 0.30 N 51 6 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.88 122.90 -4.02 0.60 N 52 6 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.21 108.30 2.91 0.30 N 53 6 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.84 108.30 3.54 0.30 N 54 6 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.35 108.30 2.05 0.30 N 55 7 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.44 108.30 3.14 0.30 N 56 7 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.02 108.30 2.72 0.30 N 57 7 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.97 108.30 2.67 0.30 N 58 7 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.34 108.30 4.04 0.30 N 59 7 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.25 108.30 2.95 0.30 N 60 7 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.86 122.90 -4.04 0.60 N 61 7 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.22 108.30 2.92 0.30 N 62 7 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.32 108.30 2.02 0.30 N 63 7 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.67 108.30 2.37 0.30 N 64 8 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.41 108.30 3.11 0.30 N 65 8 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 111.11 108.30 2.81 0.30 N 66 8 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.74 108.30 2.44 0.30 N 67 8 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.03 108.30 3.73 0.30 N 68 8 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.97 108.30 3.67 0.30 N 69 8 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.88 122.90 -4.02 0.60 N 70 8 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.27 108.30 2.97 0.30 N 71 8 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.82 108.30 3.52 0.30 N 72 8 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.28 108.30 1.98 0.30 N # 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 2 DG A 7 ? ? 0.052 'SIDE CHAIN' 2 4 DG A 7 ? ? 0.052 'SIDE CHAIN' 3 6 DG A 7 ? ? 0.049 'SIDE CHAIN' 4 7 DA A 4 ? ? 0.053 'SIDE CHAIN' 5 8 DG A 7 ? ? 0.054 'SIDE CHAIN' # 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 APN "C8'" C N N 1 APN "C7'" C N N 2 APN "O7'" O N N 3 APN "C5'" C N N 4 APN C C N N 5 APN O O N N 6 APN OXT O N N 7 APN "N4'" N N N 8 APN "C3'" C N N 9 APN "C2'" C N N 10 APN N N N N 11 APN N9 N Y N 12 APN C8 C Y N 13 APN N7 N Y N 14 APN C5 C Y N 15 APN C6 C Y N 16 APN N6 N N N 17 APN N1 N Y N 18 APN C2 C Y N 19 APN N3 N Y N 20 APN C4 C Y N 21 APN "H8'1" H N N 22 APN "H8'2" H N N 23 APN "H5'1" H N N 24 APN "H5'2" H N N 25 APN HXT H N N 26 APN "H3'1" H N N 27 APN "H3'2" H N N 28 APN "H2'1" H N N 29 APN "H2'2" H N N 30 APN H H N N 31 APN H2 H N N 32 APN H3 H N N 33 APN H8 H N N 34 APN HN61 H N N 35 APN HN62 H N N 36 APN H21 H N N 37 CPN "C8'" C N N 38 CPN "C7'" C N N 39 CPN "O7'" O N N 40 CPN "C5'" C N N 41 CPN C C N N 42 CPN O O N N 43 CPN OXT O N N 44 CPN "N4'" N N N 45 CPN "C3'" C N N 46 CPN "C2'" C N N 47 CPN N N N N 48 CPN N1 N N N 49 CPN C2 C N N 50 CPN N3 N N N 51 CPN C4 C N N 52 CPN C5 C N N 53 CPN C6 C N N 54 CPN O2 O N N 55 CPN N4 N N N 56 CPN "H8'1" H N N 57 CPN "H8'2" H N N 58 CPN "H5'1" H N N 59 CPN "H5'2" H N N 60 CPN HXT H N N 61 CPN "H3'1" H N N 62 CPN "H3'2" H N N 63 CPN "H2'1" H N N 64 CPN "H2'2" H N N 65 CPN H H N N 66 CPN H2 H N N 67 CPN H3 H N N 68 CPN H5 H N N 69 CPN H6 H N N 70 CPN HN41 H N N 71 CPN HN42 H N N 72 DA OP3 O N N 73 DA P P N N 74 DA OP1 O N N 75 DA OP2 O N N 76 DA "O5'" O N N 77 DA "C5'" C N N 78 DA "C4'" C N R 79 DA "O4'" O N N 80 DA "C3'" C N S 81 DA "O3'" O N N 82 DA "C2'" C N N 83 DA "C1'" C N R 84 DA N9 N Y N 85 DA C8 C Y N 86 DA N7 N Y N 87 DA C5 C Y N 88 DA C6 C Y N 89 DA N6 N N N 90 DA N1 N Y N 91 DA C2 C Y N 92 DA N3 N Y N 93 DA C4 C Y N 94 DA HOP3 H N N 95 DA HOP2 H N N 96 DA "H5'" H N N 97 DA "H5''" H N N 98 DA "H4'" H N N 99 DA "H3'" H N N 100 DA "HO3'" H N N 101 DA "H2'" H N N 102 DA "H2''" H N N 103 DA "H1'" H N N 104 DA H8 H N N 105 DA H61 H N N 106 DA H62 H N N 107 DA H2 H N N 108 DC OP3 O N N 109 DC P P N N 110 DC OP1 O N N 111 DC OP2 O N N 112 DC "O5'" O N N 113 DC "C5'" C N N 114 DC "C4'" C N R 115 DC "O4'" O N N 116 DC "C3'" C N S 117 DC "O3'" O N N 118 DC "C2'" C N N 119 DC "C1'" C N R 120 DC N1 N N N 121 DC C2 C N N 122 DC O2 O N N 123 DC N3 N N N 124 DC C4 C N N 125 DC N4 N N N 126 DC C5 C N N 127 DC C6 C N N 128 DC HOP3 H N N 129 DC HOP2 H N N 130 DC "H5'" H N N 131 DC "H5''" H N N 132 DC "H4'" H N N 133 DC "H3'" H N N 134 DC "HO3'" H N N 135 DC "H2'" H N N 136 DC "H2''" H N N 137 DC "H1'" H N N 138 DC H41 H N N 139 DC H42 H N N 140 DC H5 H N N 141 DC H6 H N N 142 DG OP3 O N N 143 DG P P N N 144 DG OP1 O N N 145 DG OP2 O N N 146 DG "O5'" O N N 147 DG "C5'" C N N 148 DG "C4'" C N R 149 DG "O4'" O N N 150 DG "C3'" C N S 151 DG "O3'" O N N 152 DG "C2'" C N N 153 DG "C1'" C N R 154 DG N9 N Y N 155 DG C8 C Y N 156 DG N7 N Y N 157 DG C5 C Y N 158 DG C6 C N N 159 DG O6 O N N 160 DG N1 N N N 161 DG C2 C N N 162 DG N2 N N N 163 DG N3 N N N 164 DG C4 C Y N 165 DG HOP3 H N N 166 DG HOP2 H N N 167 DG "H5'" H N N 168 DG "H5''" H N N 169 DG "H4'" H N N 170 DG "H3'" H N N 171 DG "HO3'" H N N 172 DG "H2'" H N N 173 DG "H2''" H N N 174 DG "H1'" H N N 175 DG H8 H N N 176 DG H1 H N N 177 DG H21 H N N 178 DG H22 H N N 179 DT OP3 O N N 180 DT P P N N 181 DT OP1 O N N 182 DT OP2 O N N 183 DT "O5'" O N N 184 DT "C5'" C N N 185 DT "C4'" C N R 186 DT "O4'" O N N 187 DT "C3'" C N S 188 DT "O3'" O N N 189 DT "C2'" C N N 190 DT "C1'" C N R 191 DT N1 N N N 192 DT C2 C N N 193 DT O2 O N N 194 DT N3 N N N 195 DT C4 C N N 196 DT O4 O N N 197 DT C5 C N N 198 DT C7 C N N 199 DT C6 C N N 200 DT HOP3 H N N 201 DT HOP2 H N N 202 DT "H5'" H N N 203 DT "H5''" H N N 204 DT "H4'" H N N 205 DT "H3'" H N N 206 DT "HO3'" H N N 207 DT "H2'" H N N 208 DT "H2''" H N N 209 DT "H1'" H N N 210 DT H3 H N N 211 DT H71 H N N 212 DT H72 H N N 213 DT H73 H N N 214 DT H6 H N N 215 GPN "C8'" C N N 216 GPN "C7'" C N N 217 GPN "O7'" O N N 218 GPN "C5'" C N N 219 GPN C C N N 220 GPN O O N N 221 GPN OXT O N N 222 GPN "N4'" N N N 223 GPN "C3'" C N N 224 GPN "C2'" C N N 225 GPN N N N N 226 GPN N9 N Y N 227 GPN C8 C Y N 228 GPN N7 N Y N 229 GPN C5 C Y N 230 GPN C6 C N N 231 GPN O6 O N N 232 GPN N1 N N N 233 GPN C2 C N N 234 GPN N2 N N N 235 GPN N3 N N N 236 GPN C4 C Y N 237 GPN "H8'1" H N N 238 GPN "H8'2" H N N 239 GPN "H5'1" H N N 240 GPN "H5'2" H N N 241 GPN HXT H N N 242 GPN "H3'1" H N N 243 GPN "H3'2" H N N 244 GPN "H2'1" H N N 245 GPN "H2'2" H N N 246 GPN H H N N 247 GPN H2 H N N 248 GPN H3 H N N 249 GPN H8 H N N 250 GPN HN1 H N N 251 GPN HN21 H N N 252 GPN HN22 H N N 253 NH2 N N N N 254 NH2 HN1 H N N 255 NH2 HN2 H N N 256 TPN "C8'" C N N 257 TPN "C7'" C N N 258 TPN "O7'" O N N 259 TPN "C5'" C N N 260 TPN C C N N 261 TPN O O N N 262 TPN OXT O N N 263 TPN "N4'" N N N 264 TPN "C3'" C N N 265 TPN "C2'" C N N 266 TPN N N N N 267 TPN N1 N N N 268 TPN C6 C N N 269 TPN C2 C N N 270 TPN O2 O N N 271 TPN N3 N N N 272 TPN C4 C N N 273 TPN O4 O N N 274 TPN C5 C N N 275 TPN C5M C N N 276 TPN "H8'1" H N N 277 TPN "H8'2" H N N 278 TPN "H5'1" H N N 279 TPN "H5'2" H N N 280 TPN HXT H N N 281 TPN "H3'1" H N N 282 TPN "H3'2" H N N 283 TPN "H2'1" H N N 284 TPN "H2'2" H N N 285 TPN H H N N 286 TPN H2 H N N 287 TPN H3 H N N 288 TPN H6 H N N 289 TPN HN3 H N N 290 TPN HM51 H N N 291 TPN HM52 H N N 292 TPN HM53 H N N 293 # 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 APN "C8'" "C7'" sing N N 1 APN "C8'" N9 sing N N 2 APN "C8'" "H8'1" sing N N 3 APN "C8'" "H8'2" sing N N 4 APN "C7'" "O7'" doub N N 5 APN "C7'" "N4'" sing N N 6 APN "C5'" C sing N N 7 APN "C5'" "N4'" sing N N 8 APN "C5'" "H5'1" sing N N 9 APN "C5'" "H5'2" sing N N 10 APN C O doub N N 11 APN C OXT sing N N 12 APN OXT HXT sing N N 13 APN "N4'" "C3'" sing N N 14 APN "C3'" "C2'" sing N N 15 APN "C3'" "H3'1" sing N N 16 APN "C3'" "H3'2" sing N N 17 APN "C2'" N sing N N 18 APN "C2'" "H2'1" sing N N 19 APN "C2'" "H2'2" sing N N 20 APN N H sing N N 21 APN N H2 sing N N 22 APN N H3 sing N N 23 APN N9 C8 sing Y N 24 APN N9 C4 sing Y N 25 APN C8 N7 doub Y N 26 APN C8 H8 sing N N 27 APN N7 C5 sing Y N 28 APN C5 C6 sing Y N 29 APN C5 C4 doub Y N 30 APN C6 N6 sing N N 31 APN C6 N1 doub Y N 32 APN N6 HN61 sing N N 33 APN N6 HN62 sing N N 34 APN N1 C2 sing Y N 35 APN C2 N3 doub Y N 36 APN C2 H21 sing N N 37 APN N3 C4 sing Y N 38 CPN "C8'" "C7'" sing N N 39 CPN "C8'" N1 sing N N 40 CPN "C8'" "H8'1" sing N N 41 CPN "C8'" "H8'2" sing N N 42 CPN "C7'" "O7'" doub N N 43 CPN "C7'" "N4'" sing N N 44 CPN "C5'" C sing N N 45 CPN "C5'" "N4'" sing N N 46 CPN "C5'" "H5'1" sing N N 47 CPN "C5'" "H5'2" sing N N 48 CPN C O doub N N 49 CPN C OXT sing N N 50 CPN OXT HXT sing N N 51 CPN "N4'" "C3'" sing N N 52 CPN "C3'" "C2'" sing N N 53 CPN "C3'" "H3'1" sing N N 54 CPN "C3'" "H3'2" sing N N 55 CPN "C2'" N sing N N 56 CPN "C2'" "H2'1" sing N N 57 CPN "C2'" "H2'2" sing N N 58 CPN N H sing N N 59 CPN N H2 sing N N 60 CPN N H3 sing N N 61 CPN N1 C2 sing N N 62 CPN N1 C6 sing N N 63 CPN C2 N3 sing N N 64 CPN C2 O2 doub N N 65 CPN N3 C4 doub N N 66 CPN C4 C5 sing N N 67 CPN C4 N4 sing N N 68 CPN C5 C6 doub N N 69 CPN C5 H5 sing N N 70 CPN C6 H6 sing N N 71 CPN N4 HN41 sing N N 72 CPN N4 HN42 sing N N 73 DA OP3 P sing N N 74 DA OP3 HOP3 sing N N 75 DA P OP1 doub N N 76 DA P OP2 sing N N 77 DA P "O5'" sing N N 78 DA OP2 HOP2 sing N N 79 DA "O5'" "C5'" sing N N 80 DA "C5'" "C4'" sing N N 81 DA "C5'" "H5'" sing N N 82 DA "C5'" "H5''" sing N N 83 DA "C4'" "O4'" sing N N 84 DA "C4'" "C3'" sing N N 85 DA "C4'" "H4'" sing N N 86 DA "O4'" "C1'" sing N N 87 DA "C3'" "O3'" sing N N 88 DA "C3'" "C2'" sing N N 89 DA "C3'" "H3'" sing N N 90 DA "O3'" "HO3'" sing N N 91 DA "C2'" "C1'" sing N N 92 DA "C2'" "H2'" sing N N 93 DA "C2'" "H2''" sing N N 94 DA "C1'" N9 sing N N 95 DA "C1'" "H1'" sing N N 96 DA N9 C8 sing Y N 97 DA N9 C4 sing Y N 98 DA C8 N7 doub Y N 99 DA C8 H8 sing N N 100 DA N7 C5 sing Y N 101 DA C5 C6 sing Y N 102 DA C5 C4 doub Y N 103 DA C6 N6 sing N N 104 DA C6 N1 doub Y N 105 DA N6 H61 sing N N 106 DA N6 H62 sing N N 107 DA N1 C2 sing Y N 108 DA C2 N3 doub Y N 109 DA C2 H2 sing N N 110 DA N3 C4 sing Y N 111 DC OP3 P sing N N 112 DC OP3 HOP3 sing N N 113 DC P OP1 doub N N 114 DC P OP2 sing N N 115 DC P "O5'" sing N N 116 DC OP2 HOP2 sing N N 117 DC "O5'" "C5'" sing N N 118 DC "C5'" "C4'" sing N N 119 DC "C5'" "H5'" sing N N 120 DC "C5'" "H5''" sing N N 121 DC "C4'" "O4'" sing N N 122 DC "C4'" "C3'" sing N N 123 DC "C4'" "H4'" sing N N 124 DC "O4'" "C1'" sing N N 125 DC "C3'" "O3'" sing N N 126 DC "C3'" "C2'" sing N N 127 DC "C3'" "H3'" sing N N 128 DC "O3'" "HO3'" sing N N 129 DC "C2'" "C1'" sing N N 130 DC "C2'" "H2'" sing N N 131 DC "C2'" "H2''" sing N N 132 DC "C1'" N1 sing N N 133 DC "C1'" "H1'" sing N N 134 DC N1 C2 sing N N 135 DC N1 C6 sing N N 136 DC C2 O2 doub N N 137 DC C2 N3 sing N N 138 DC N3 C4 doub N N 139 DC C4 N4 sing N N 140 DC C4 C5 sing N N 141 DC N4 H41 sing N N 142 DC N4 H42 sing N N 143 DC C5 C6 doub N N 144 DC C5 H5 sing N N 145 DC C6 H6 sing N N 146 DG OP3 P sing N N 147 DG OP3 HOP3 sing N N 148 DG P OP1 doub N N 149 DG P OP2 sing N N 150 DG P "O5'" sing N N 151 DG OP2 HOP2 sing N N 152 DG "O5'" "C5'" sing N N 153 DG "C5'" "C4'" sing N N 154 DG "C5'" "H5'" sing N N 155 DG "C5'" "H5''" sing N N 156 DG "C4'" "O4'" sing N N 157 DG "C4'" "C3'" sing N N 158 DG "C4'" "H4'" sing N N 159 DG "O4'" "C1'" sing N N 160 DG "C3'" "O3'" sing N N 161 DG "C3'" "C2'" sing N N 162 DG "C3'" "H3'" sing N N 163 DG "O3'" "HO3'" sing N N 164 DG "C2'" "C1'" sing N N 165 DG "C2'" "H2'" sing N N 166 DG "C2'" "H2''" sing N N 167 DG "C1'" N9 sing N N 168 DG "C1'" "H1'" sing N N 169 DG N9 C8 sing Y N 170 DG N9 C4 sing Y N 171 DG C8 N7 doub Y N 172 DG C8 H8 sing N N 173 DG N7 C5 sing Y N 174 DG C5 C6 sing N N 175 DG C5 C4 doub Y N 176 DG C6 O6 doub N N 177 DG C6 N1 sing N N 178 DG N1 C2 sing N N 179 DG N1 H1 sing N N 180 DG C2 N2 sing N N 181 DG C2 N3 doub N N 182 DG N2 H21 sing N N 183 DG N2 H22 sing N N 184 DG N3 C4 sing N N 185 DT OP3 P sing N N 186 DT OP3 HOP3 sing N N 187 DT P OP1 doub N N 188 DT P OP2 sing N N 189 DT P "O5'" sing N N 190 DT OP2 HOP2 sing N N 191 DT "O5'" "C5'" sing N N 192 DT "C5'" "C4'" sing N N 193 DT "C5'" "H5'" sing N N 194 DT "C5'" "H5''" sing N N 195 DT "C4'" "O4'" sing N N 196 DT "C4'" "C3'" sing N N 197 DT "C4'" "H4'" sing N N 198 DT "O4'" "C1'" sing N N 199 DT "C3'" "O3'" sing N N 200 DT "C3'" "C2'" sing N N 201 DT "C3'" "H3'" sing N N 202 DT "O3'" "HO3'" sing N N 203 DT "C2'" "C1'" sing N N 204 DT "C2'" "H2'" sing N N 205 DT "C2'" "H2''" sing N N 206 DT "C1'" N1 sing N N 207 DT "C1'" "H1'" sing N N 208 DT N1 C2 sing N N 209 DT N1 C6 sing N N 210 DT C2 O2 doub N N 211 DT C2 N3 sing N N 212 DT N3 C4 sing N N 213 DT N3 H3 sing N N 214 DT C4 O4 doub N N 215 DT C4 C5 sing N N 216 DT C5 C7 sing N N 217 DT C5 C6 doub N N 218 DT C7 H71 sing N N 219 DT C7 H72 sing N N 220 DT C7 H73 sing N N 221 DT C6 H6 sing N N 222 GPN "C8'" "C7'" sing N N 223 GPN "C8'" N9 sing N N 224 GPN "C8'" "H8'1" sing N N 225 GPN "C8'" "H8'2" sing N N 226 GPN "C7'" "O7'" doub N N 227 GPN "C7'" "N4'" sing N N 228 GPN "C5'" C sing N N 229 GPN "C5'" "N4'" sing N N 230 GPN "C5'" "H5'1" sing N N 231 GPN "C5'" "H5'2" sing N N 232 GPN C O doub N N 233 GPN C OXT sing N N 234 GPN OXT HXT sing N N 235 GPN "N4'" "C3'" sing N N 236 GPN "C3'" "C2'" sing N N 237 GPN "C3'" "H3'1" sing N N 238 GPN "C3'" "H3'2" sing N N 239 GPN "C2'" N sing N N 240 GPN "C2'" "H2'1" sing N N 241 GPN "C2'" "H2'2" sing N N 242 GPN N H sing N N 243 GPN N H2 sing N N 244 GPN N H3 sing N N 245 GPN N9 C8 sing Y N 246 GPN N9 C4 sing Y N 247 GPN C8 N7 doub Y N 248 GPN C8 H8 sing N N 249 GPN N7 C5 sing Y N 250 GPN C5 C6 sing N N 251 GPN C5 C4 doub Y N 252 GPN C6 O6 doub N N 253 GPN C6 N1 sing N N 254 GPN N1 C2 sing N N 255 GPN N1 HN1 sing N N 256 GPN C2 N2 sing N N 257 GPN C2 N3 doub N N 258 GPN N2 HN21 sing N N 259 GPN N2 HN22 sing N N 260 GPN N3 C4 sing N N 261 NH2 N HN1 sing N N 262 NH2 N HN2 sing N N 263 TPN "C8'" "C7'" sing N N 264 TPN "C8'" N1 sing N N 265 TPN "C8'" "H8'1" sing N N 266 TPN "C8'" "H8'2" sing N N 267 TPN "C7'" "O7'" doub N N 268 TPN "C7'" "N4'" sing N N 269 TPN "C5'" C sing N N 270 TPN "C5'" "N4'" sing N N 271 TPN "C5'" "H5'1" sing N N 272 TPN "C5'" "H5'2" sing N N 273 TPN C O doub N N 274 TPN C OXT sing N N 275 TPN OXT HXT sing N N 276 TPN "N4'" "C3'" sing N N 277 TPN "C3'" "C2'" sing N N 278 TPN "C3'" "H3'1" sing N N 279 TPN "C3'" "H3'2" sing N N 280 TPN "C2'" N sing N N 281 TPN "C2'" "H2'1" sing N N 282 TPN "C2'" "H2'2" sing N N 283 TPN N H sing N N 284 TPN N H2 sing N N 285 TPN N H3 sing N N 286 TPN N1 C6 sing N N 287 TPN N1 C2 sing N N 288 TPN C6 C5 doub N N 289 TPN C6 H6 sing N N 290 TPN C2 O2 doub N N 291 TPN C2 N3 sing N N 292 TPN N3 C4 sing N N 293 TPN N3 HN3 sing N N 294 TPN C4 O4 doub N N 295 TPN C4 C5 sing N N 296 TPN C5 C5M sing N N 297 TPN C5M HM51 sing N N 298 TPN C5M HM52 sing N N 299 TPN C5M HM53 sing N N 300 # _ndb_struct_conf_na.entry_id 1PDT _ndb_struct_conf_na.feature 'double 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 DG 1 1_555 B CPN 8 1_555 -0.745 -0.311 0.277 15.617 15.050 -1.845 1 A_DG1:CPN16_B A 1 ? B 16 ? 19 1 1 A DA 2 1_555 B TPN 7 1_555 -0.076 -0.118 -0.297 17.882 -9.948 -4.890 2 A_DA2:TPN15_B A 2 ? B 15 ? 20 1 1 A DC 3 1_555 B GPN 6 1_555 0.673 -0.249 -0.455 20.844 -5.040 -2.134 3 A_DC3:GPN14_B A 3 ? B 14 ? 19 1 1 A DA 4 1_555 B TPN 5 1_555 0.304 -0.128 -0.038 16.845 -4.901 -2.221 4 A_DA4:TPN13_B A 4 ? B 13 ? 20 1 1 A DT 5 1_555 B APN 4 1_555 -0.352 -0.070 -0.355 14.225 5.775 -8.447 5 A_DT5:APN12_B A 5 ? B 12 ? 20 1 1 A DA 6 1_555 B TPN 3 1_555 0.490 -0.130 -0.047 8.040 -4.137 -1.613 6 A_DA6:TPN11_B A 6 ? B 11 ? 20 1 1 A DG 7 1_555 B CPN 2 1_555 -0.324 -0.185 -0.301 -5.812 -15.283 0.159 7 A_DG7:CPN10_B A 7 ? B 10 ? 19 1 1 A DC 8 1_555 B GPN 1 1_555 0.671 -0.147 -0.435 37.293 -25.743 -1.239 8 A_DC8:GPN9_B A 8 ? B 9 ? 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 DG 1 1_555 B CPN 8 1_555 A DA 2 1_555 B TPN 7 1_555 -0.411 -2.136 3.243 2.984 -3.939 32.163 -3.109 1.269 3.422 -7.058 -5.347 32.530 1 AA_DG1DA2:TPN15CPN16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A DA 2 1_555 B TPN 7 1_555 A DC 3 1_555 B GPN 6 1_555 -0.907 -1.681 3.188 -3.941 3.031 29.783 -3.823 0.966 3.098 5.845 7.600 30.186 2 AA_DA2DC3:GPN14TPN15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DC 3 1_555 B GPN 6 1_555 A DA 4 1_555 B TPN 5 1_555 -1.661 -2.643 3.254 -11.708 15.368 22.376 -8.077 1.067 1.773 32.820 25.003 29.482 3 AA_DC3DA4:TPN13GPN14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DA 4 1_555 B TPN 5 1_555 A DT 5 1_555 B APN 4 1_555 -0.692 -3.002 3.337 -2.403 2.501 25.460 -7.446 0.889 3.084 5.642 5.421 25.692 4 AA_DA4DT5:APN12TPN13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A DT 5 1_555 B APN 4 1_555 A DA 6 1_555 B TPN 3 1_555 0.146 -1.873 3.745 -4.037 -15.320 28.038 0.164 -1.199 4.136 -28.887 7.612 32.126 5 AA_DT5DA6:TPN11APN12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A DA 6 1_555 B TPN 3 1_555 A DG 7 1_555 B CPN 2 1_555 -0.834 -1.701 3.691 0.623 -2.874 30.080 -2.592 1.746 3.815 -5.522 -1.197 30.220 6 AA_DA6DG7:CPN10TPN11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DG 7 1_555 B CPN 2 1_555 A DC 8 1_555 B GPN 1 1_555 -1.114 -0.206 2.331 -7.951 -6.421 27.777 0.641 0.888 2.530 -12.836 15.896 29.563 7 AA_DG7DC8:GPN9CPN10_BB A 7 ? B 10 ? A 8 ? B 9 ? #