data_2KK5 # _entry.id 2KK5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 2KK5 pdb_00002kk5 10.2210/pdb2kk5/pdb RCSB RCSB101220 ? ? WWPDB D_1000101220 ? ? # 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 2009-07-21 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 4 'Structure model' 1 3 2024-05-22 # _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' '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_spectrometer 3 3 'Structure model' pdbx_struct_assembly 4 3 'Structure model' pdbx_struct_oper_list 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site 7 4 'Structure model' chem_comp_atom 8 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_spectrometer.model' 4 3 'Structure model' '_struct_conn.pdbx_dist_value' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 7 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KK5 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-06-15 _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 'Patra, A.' 1 'Richert, C.' 2 # _citation.id primary _citation.title ;High fidelity base pairing at the 3'-terminus. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 131 _citation.page_first 12671 _citation.page_last 12681 _citation.year 2009 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19722718 _citation.pdbx_database_id_DOI 10.1021/ja9033654 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Patra, A.' 1 ? primary 'Richert, C.' 2 ? # 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 "5'-D(*AP*CP*GP*CP*GP*(2AU))-3'" 1810.206 2 ? ? ? ? 2 non-polymer syn 9,10-dioxo-9,10-dihydroanthracene-2-carboxamide 251.237 2 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DA)(DC)(DG)(DC)(DG)(2AU)' _entity_poly.pdbx_seq_one_letter_code_can ACGCGU _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 9,10-dioxo-9,10-dihydroanthracene-2-carboxamide _pdbx_entity_nonpoly.comp_id AQC # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DG n 1 4 DC n 1 5 DG n 1 6 2AU n # 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 2AU 'RNA linking' n "2'-AMINOURIDINE" ? 'C9 H14 N3 O8 P' 323.197 AQC non-polymer . 9,10-dioxo-9,10-dihydroanthracene-2-carboxamide ? 'C15 H9 N O3' 251.237 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 # 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 DA 1 1 1 DA DA A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 2AU 6 6 6 2AU 2AU A . n B 1 1 DA 1 1 1 DA DA B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DG 3 3 3 DG DG B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 2AU 6 6 6 2AU 2AU B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 AQC 1 7 7 AQC AQC A . D 2 AQC 1 7 7 AQC AQC B . # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KK5 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KK5 _struct.title ;High Fidelity Base Pairing at the 3'-Terminus ; _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KK5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Anthraquinone-linked DNA, DNA' # 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 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2KK5 _struct_ref.pdbx_db_accession 2KK5 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ACGCGU _struct_ref.pdbx_db_isoform ? # 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 2KK5 A 1 ? 6 ? 2KK5 1 ? 6 ? 1 6 2 1 2KK5 B 1 ? 6 ? 2KK5 1 ? 6 ? 1 6 # _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,C,D # _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 # _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 ? A DG 5 "O3'" ? ? ? 1_555 A 2AU 6 P ? ? A DG 5 A 2AU 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale none ? A 2AU 6 "C2'" ? ? ? 1_555 C AQC . "N2'" ? ? A 2AU 6 A AQC 7 1_555 ? ? ? ? ? ? ? 1.455 ? ? covale3 covale both ? B DG 5 "O3'" ? ? ? 1_555 B 2AU 6 P ? ? B DG 5 B 2AU 6 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale4 covale none ? B 2AU 6 "C2'" ? ? ? 1_555 D AQC . "N2'" ? ? B 2AU 6 B AQC 7 1_555 ? ? ? ? ? ? ? 1.454 ? ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 2 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 2 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 2 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 5 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 5 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 5 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A AQC 7 ? 4 'BINDING SITE FOR RESIDUE AQC A 7' AC2 Software B AQC 7 ? 4 'BINDING SITE FOR RESIDUE AQC B 7' 1 ? ? ? ? ? ? ? # 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 4 DG A 5 ? DG A 5 . ? 1_555 ? 2 AC1 4 2AU A 6 ? 2AU A 6 . ? 1_555 ? 3 AC1 4 DA B 1 ? DA B 1 . ? 1_555 ? 4 AC1 4 DC B 2 ? DC B 2 . ? 1_555 ? 5 AC2 4 DA A 1 ? DA A 1 . ? 1_555 ? 6 AC2 4 DC A 2 ? DC A 2 . ? 1_555 ? 7 AC2 4 DG B 5 ? DG B 5 . ? 1_555 ? 8 AC2 4 2AU B 6 ? 2AU B 6 . ? 1_555 ? # 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 A 2AU 6 A 2AU 6 ? U "2'-AMINOURIDINE" 2 B 2AU 6 B 2AU 6 ? U "2'-AMINOURIDINE" # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'INTERCALATION, COVALENT' # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 80 _pdbx_nmr_ensemble.conformers_submitted_total_number 3 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KK5 _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 2KK5 _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_sample_details.contents '2 mM Anthraquinon capped DNA duplex, 100% D2O, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O, 90% H2O/10% D2O' # _pdbx_nmr_exptl_sample.component 'Anthraquinon capped DNA duplex-1' _pdbx_nmr_exptl_sample.concentration 2 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.15 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D DQF-COSY' # _pdbx_nmr_refine.entry_id 2KK5 _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.1 1 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.1 2 # 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 2AU OP3 O N N 1 2AU P P N N 2 2AU OP1 O N N 3 2AU "O5'" O N N 4 2AU "C5'" C N N 5 2AU "C4'" C N R 6 2AU "O4'" O N N 7 2AU "C3'" C N S 8 2AU "O3'" O N N 9 2AU "C2'" C N R 10 2AU "C1'" C N R 11 2AU N1 N N N 12 2AU C2 C N N 13 2AU O2 O N N 14 2AU N3 N N N 15 2AU C4 C N N 16 2AU O4 O N N 17 2AU C5 C N N 18 2AU C6 C N N 19 2AU "N2'" N N N 20 2AU H1P1 H N N 21 2AU "H5'" H N N 22 2AU "H5''" H N N 23 2AU "H4'" H N N 24 2AU "H3'" H N N 25 2AU "HO3'" H N N 26 2AU "H2'" H N N 27 2AU "H1'" H N N 28 2AU H3 H N N 29 2AU H5 H N N 30 2AU H6 H N N 31 2AU HA1 H N N 32 2AU "H2''" H N N 33 2AU OP2 O N N 34 2AU H2P1 H N N 35 AQC C4A C Y N 36 AQC C1A C Y N 37 AQC C9 C N N 38 AQC C8A C Y N 39 AQC C5A C Y N 40 AQC C10 C N N 41 AQC C4 C Y N 42 AQC C3 C Y N 43 AQC C2 C Y N 44 AQC C1 C Y N 45 AQC C8 C Y N 46 AQC C5 C Y N 47 AQC C7 C Y N 48 AQC C6 C Y N 49 AQC C1L C N N 50 AQC "N2'" N N N 51 AQC O9 O N N 52 AQC O10 O N N 53 AQC O1L O N N 54 AQC H4 H N N 55 AQC H3 H N N 56 AQC H1 H N N 57 AQC H8 H N N 58 AQC H5 H N N 59 AQC H7 H N N 60 AQC H6 H N N 61 AQC "HN2'" H N N 62 AQC HN2A H N N 63 DA OP3 O N N 64 DA P P N N 65 DA OP1 O N N 66 DA OP2 O N N 67 DA "O5'" O N N 68 DA "C5'" C N N 69 DA "C4'" C N R 70 DA "O4'" O N N 71 DA "C3'" C N S 72 DA "O3'" O N N 73 DA "C2'" C N N 74 DA "C1'" C N R 75 DA N9 N Y N 76 DA C8 C Y N 77 DA N7 N Y N 78 DA C5 C Y N 79 DA C6 C Y N 80 DA N6 N N N 81 DA N1 N Y N 82 DA C2 C Y N 83 DA N3 N Y N 84 DA C4 C Y N 85 DA HOP3 H N N 86 DA HOP2 H N N 87 DA "H5'" H N N 88 DA "H5''" H N N 89 DA "H4'" H N N 90 DA "H3'" H N N 91 DA "HO3'" H N N 92 DA "H2'" H N N 93 DA "H2''" H N N 94 DA "H1'" H N N 95 DA H8 H N N 96 DA H61 H N N 97 DA H62 H N N 98 DA H2 H N N 99 DC OP3 O N N 100 DC P P N N 101 DC OP1 O N N 102 DC OP2 O N N 103 DC "O5'" O N N 104 DC "C5'" C N N 105 DC "C4'" C N R 106 DC "O4'" O N N 107 DC "C3'" C N S 108 DC "O3'" O N N 109 DC "C2'" C N N 110 DC "C1'" C N R 111 DC N1 N N N 112 DC C2 C N N 113 DC O2 O N N 114 DC N3 N N N 115 DC C4 C N N 116 DC N4 N N N 117 DC C5 C N N 118 DC C6 C N N 119 DC HOP3 H N N 120 DC HOP2 H N N 121 DC "H5'" H N N 122 DC "H5''" H N N 123 DC "H4'" H N N 124 DC "H3'" H N N 125 DC "HO3'" H N N 126 DC "H2'" H N N 127 DC "H2''" H N N 128 DC "H1'" H N N 129 DC H41 H N N 130 DC H42 H N N 131 DC H5 H N N 132 DC H6 H N N 133 DG OP3 O N N 134 DG P P N N 135 DG OP1 O N N 136 DG OP2 O N N 137 DG "O5'" O N N 138 DG "C5'" C N N 139 DG "C4'" C N R 140 DG "O4'" O N N 141 DG "C3'" C N S 142 DG "O3'" O N N 143 DG "C2'" C N N 144 DG "C1'" C N R 145 DG N9 N Y N 146 DG C8 C Y N 147 DG N7 N Y N 148 DG C5 C Y N 149 DG C6 C N N 150 DG O6 O N N 151 DG N1 N N N 152 DG C2 C N N 153 DG N2 N N N 154 DG N3 N N N 155 DG C4 C Y N 156 DG HOP3 H N N 157 DG HOP2 H N N 158 DG "H5'" H N N 159 DG "H5''" H N N 160 DG "H4'" H N N 161 DG "H3'" H N N 162 DG "HO3'" H N N 163 DG "H2'" H N N 164 DG "H2''" H N N 165 DG "H1'" H N N 166 DG H8 H N N 167 DG H1 H N N 168 DG H21 H N N 169 DG H22 H N N 170 # 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 2AU OP3 P doub N N 1 2AU P OP1 sing N N 2 2AU P "O5'" sing N N 3 2AU OP1 H1P1 sing N N 4 2AU "O5'" "C5'" sing N N 5 2AU "C5'" "C4'" sing N N 6 2AU "C5'" "H5'" sing N N 7 2AU "C5'" "H5''" sing N N 8 2AU "C4'" "O4'" sing N N 9 2AU "C4'" "C3'" sing N N 10 2AU "C4'" "H4'" sing N N 11 2AU "O4'" "C1'" sing N N 12 2AU "C3'" "O3'" sing N N 13 2AU "C3'" "C2'" sing N N 14 2AU "C3'" "H3'" sing N N 15 2AU "O3'" "HO3'" sing N N 16 2AU "C2'" "C1'" sing N N 17 2AU "C2'" "N2'" sing N N 18 2AU "C2'" "H2'" sing N N 19 2AU "C1'" N1 sing N N 20 2AU "C1'" "H1'" sing N N 21 2AU N1 C2 sing N N 22 2AU N1 C6 sing N N 23 2AU C2 O2 doub N N 24 2AU C2 N3 sing N N 25 2AU N3 C4 sing N N 26 2AU N3 H3 sing N N 27 2AU C4 O4 doub N N 28 2AU C4 C5 sing N N 29 2AU C5 C6 doub N N 30 2AU C5 H5 sing N N 31 2AU C6 H6 sing N N 32 2AU "N2'" HA1 sing N N 33 2AU "N2'" "H2''" sing N N 34 2AU OP2 P sing N N 35 2AU OP2 H2P1 sing N N 36 AQC C4 C4A doub Y N 37 AQC C4A C10 sing N N 38 AQC C4A C1A sing Y N 39 AQC C1 C1A doub Y N 40 AQC C1A C9 sing N N 41 AQC C9 C8A sing N N 42 AQC C9 O9 doub N N 43 AQC C5A C8A doub Y N 44 AQC C8A C8 sing Y N 45 AQC C10 C5A sing N N 46 AQC C5A C5 sing Y N 47 AQC O10 C10 doub N N 48 AQC H4 C4 sing N N 49 AQC C3 C4 sing Y N 50 AQC H3 C3 sing N N 51 AQC C3 C2 doub Y N 52 AQC C1L C2 sing N N 53 AQC C2 C1 sing Y N 54 AQC C1 H1 sing N N 55 AQC C8 C7 doub Y N 56 AQC C8 H8 sing N N 57 AQC H5 C5 sing N N 58 AQC C5 C6 doub Y N 59 AQC C6 C7 sing Y N 60 AQC C7 H7 sing N N 61 AQC C6 H6 sing N N 62 AQC "N2'" C1L sing N N 63 AQC C1L O1L doub N N 64 AQC "HN2'" "N2'" sing N N 65 AQC "N2'" HN2A sing N N 66 DA OP3 P sing N N 67 DA OP3 HOP3 sing N N 68 DA P OP1 doub N N 69 DA P OP2 sing N N 70 DA P "O5'" sing N N 71 DA OP2 HOP2 sing N N 72 DA "O5'" "C5'" sing N N 73 DA "C5'" "C4'" sing N N 74 DA "C5'" "H5'" sing N N 75 DA "C5'" "H5''" sing N N 76 DA "C4'" "O4'" sing N N 77 DA "C4'" "C3'" sing N N 78 DA "C4'" "H4'" sing N N 79 DA "O4'" "C1'" sing N N 80 DA "C3'" "O3'" sing N N 81 DA "C3'" "C2'" sing N N 82 DA "C3'" "H3'" sing N N 83 DA "O3'" "HO3'" sing N N 84 DA "C2'" "C1'" sing N N 85 DA "C2'" "H2'" sing N N 86 DA "C2'" "H2''" sing N N 87 DA "C1'" N9 sing N N 88 DA "C1'" "H1'" sing N N 89 DA N9 C8 sing Y N 90 DA N9 C4 sing Y N 91 DA C8 N7 doub Y N 92 DA C8 H8 sing N N 93 DA N7 C5 sing Y N 94 DA C5 C6 sing Y N 95 DA C5 C4 doub Y N 96 DA C6 N6 sing N N 97 DA C6 N1 doub Y N 98 DA N6 H61 sing N N 99 DA N6 H62 sing N N 100 DA N1 C2 sing Y N 101 DA C2 N3 doub Y N 102 DA C2 H2 sing N N 103 DA N3 C4 sing Y N 104 DC OP3 P sing N N 105 DC OP3 HOP3 sing N N 106 DC P OP1 doub N N 107 DC P OP2 sing N N 108 DC P "O5'" sing N N 109 DC OP2 HOP2 sing N N 110 DC "O5'" "C5'" sing N N 111 DC "C5'" "C4'" sing N N 112 DC "C5'" "H5'" sing N N 113 DC "C5'" "H5''" sing N N 114 DC "C4'" "O4'" sing N N 115 DC "C4'" "C3'" sing N N 116 DC "C4'" "H4'" sing N N 117 DC "O4'" "C1'" sing N N 118 DC "C3'" "O3'" sing N N 119 DC "C3'" "C2'" sing N N 120 DC "C3'" "H3'" sing N N 121 DC "O3'" "HO3'" sing N N 122 DC "C2'" "C1'" sing N N 123 DC "C2'" "H2'" sing N N 124 DC "C2'" "H2''" sing N N 125 DC "C1'" N1 sing N N 126 DC "C1'" "H1'" sing N N 127 DC N1 C2 sing N N 128 DC N1 C6 sing N N 129 DC C2 O2 doub N N 130 DC C2 N3 sing N N 131 DC N3 C4 doub N N 132 DC C4 N4 sing N N 133 DC C4 C5 sing N N 134 DC N4 H41 sing N N 135 DC N4 H42 sing N N 136 DC C5 C6 doub N N 137 DC C5 H5 sing N N 138 DC C6 H6 sing N N 139 DG OP3 P sing N N 140 DG OP3 HOP3 sing N N 141 DG P OP1 doub N N 142 DG P OP2 sing N N 143 DG P "O5'" sing N N 144 DG OP2 HOP2 sing N N 145 DG "O5'" "C5'" sing N N 146 DG "C5'" "C4'" sing N N 147 DG "C5'" "H5'" sing N N 148 DG "C5'" "H5''" sing N N 149 DG "C4'" "O4'" sing N N 150 DG "C4'" "C3'" sing N N 151 DG "C4'" "H4'" sing N N 152 DG "O4'" "C1'" sing N N 153 DG "C3'" "O3'" sing N N 154 DG "C3'" "C2'" sing N N 155 DG "C3'" "H3'" sing N N 156 DG "O3'" "HO3'" sing N N 157 DG "C2'" "C1'" sing N N 158 DG "C2'" "H2'" sing N N 159 DG "C2'" "H2''" sing N N 160 DG "C1'" N9 sing N N 161 DG "C1'" "H1'" sing N N 162 DG N9 C8 sing Y N 163 DG N9 C4 sing Y N 164 DG C8 N7 doub Y N 165 DG C8 H8 sing N N 166 DG N7 C5 sing Y N 167 DG C5 C6 sing N N 168 DG C5 C4 doub Y N 169 DG C6 O6 doub N N 170 DG C6 N1 sing N N 171 DG N1 C2 sing N N 172 DG N1 H1 sing N N 173 DG C2 N2 sing N N 174 DG C2 N3 doub N N 175 DG N2 H21 sing N N 176 DG N2 H22 sing N N 177 DG N3 C4 sing N N 178 # _ndb_struct_conf_na.entry_id 2KK5 _ndb_struct_conf_na.feature 'b-form 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 DC 2 1_555 B DG 5 1_555 1.176 -0.363 0.219 -11.014 -4.496 0.113 1 A_DC2:DG5_B A 2 ? B 5 ? 19 1 1 A DG 3 1_555 B DC 4 1_555 -0.412 -0.233 -0.135 -3.727 -0.886 0.415 2 A_DG3:DC4_B A 3 ? B 4 ? 19 1 1 A DC 4 1_555 B DG 3 1_555 0.412 -0.233 -0.134 3.725 -0.883 0.412 3 A_DC4:DG3_B A 4 ? B 3 ? 19 1 1 A DG 5 1_555 B DC 2 1_555 -1.176 -0.363 0.218 10.996 -4.482 0.107 4 A_DG5:DC2_B A 5 ? B 2 ? 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 DC 2 1_555 B DG 5 1_555 A DG 3 1_555 B DC 4 1_555 0.282 0.850 2.962 4.226 16.354 23.079 -2.005 0.391 2.926 35.421 -9.152 28.532 1 AA_DC2DG3:DC4DG5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DG 3 1_555 B DC 4 1_555 A DC 4 1_555 B DG 3 1_555 0.000 0.855 2.896 -0.003 12.897 43.335 0.045 0.000 3.019 17.021 0.004 45.125 2 AA_DG3DC4:DG3DC4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DC 4 1_555 B DG 3 1_555 A DG 5 1_555 B DC 2 1_555 -0.282 0.850 2.963 -4.225 16.347 23.079 -2.003 -0.391 2.927 35.409 9.152 28.528 3 AA_DC4DG5:DC2DG3_BB A 4 ? B 3 ? A 5 ? B 2 ? # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _atom_sites.entry_id 2KK5 _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_