data_1NP5 # _entry.id 1NP5 # _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 1NP5 pdb_00001np5 10.2210/pdb1np5/pdb RCSB RCSB018071 ? ? WWPDB D_1000018071 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NP5 _pdbx_database_status.recvd_initial_deposition_date 2003-01-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _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 'Zheng, M.' 1 'Han, X.' 2 'Gao, X.' 3 # _citation.id primary _citation.title ;Strand polarity of trinucleotide repeat sequences: NMR studies of parallel/anti-pararell duplex,{d(GAC)3}2 ; _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zheng, M.' 1 ? primary 'Han, X.' 2 ? primary 'Gao, X.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*GP*AP*CP*GP*AP*CP*GP*AP*C)-3'" _entity.formula_weight 2749.826 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DA)(DC)(DG)(DA)(DC)(DG)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GACGACGAC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DA n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DA n 1 9 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence is found in triplet repeat expansion involving neurogenetic diseases.' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1NP5 _struct_ref.pdbx_db_accession 1NP5 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1NP5 A 1 ? 9 ? 1NP5 1 ? 9 ? 1 9 2 1 1NP5 B 1 ? 9 ? 1NP5 101 ? 109 ? 101 109 # 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 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_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' 3 1 1 DQF-COSY 4 1 1 COSY-35 5 1 1 '1H-31P COSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 273 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 4.7 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ;2 mM 5'-d(GACGACGAC), 0.1 M NaCl, 10 mM Sodium Phosphate, 0.1 mM EDTA ; _pdbx_nmr_sample_details.solvent_system '90 % H20, 10 % D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AMX _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1NP5 _pdbx_nmr_refine.method 'distance geometry, restraint molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1NP5 _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques' # _pdbx_nmr_ensemble.entry_id 1NP5 _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1NP5 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal UXNMR 940101 processing Bruker 1 Felix 95 processing Accelrys 2 X-PLOR 3.01 'structure solution' Brunger 3 MARDIGRAS 3.0 refinement 'Borgias, B.A.' 4 # _exptl.entry_id 1NP5 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1NP5 _struct.title '(GAC)3 parallel duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1NP5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA trinucleotide repeat, parallel duplex, homo-basepair mismatch, NMR solution structure, 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 ? # _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 hydrog1 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DG 1 N3 ? ? A DG 1 B DG 101 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 N3 ? ? ? 1_555 B DG 1 N2 ? ? A DG 1 B DG 101 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog3 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DA 2 N7 ? ? A DA 2 B DA 102 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog4 hydrog ? ? A DA 2 N7 ? ? ? 1_555 B DA 2 N6 ? ? A DA 2 B DA 102 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DC 3 O2 ? ? A DC 3 B DC 103 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DC 3 N4 ? ? A DC 3 B DC 103 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DG 4 N3 ? ? A DG 4 B DG 104 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog8 hydrog ? ? A DG 4 N3 ? ? ? 1_555 B DG 4 N2 ? ? A DG 4 B DG 104 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog9 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DA 5 N7 ? ? A DA 5 B DA 105 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog10 hydrog ? ? A DA 5 N7 ? ? ? 1_555 B DA 5 N6 ? ? A DA 5 B DA 105 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog11 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DC 6 O2 ? ? A DC 6 B DC 106 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog12 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DC 6 N4 ? ? A DC 6 B DC 106 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog13 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DG 7 N3 ? ? A DG 7 B DG 107 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog14 hydrog ? ? A DG 7 N3 ? ? ? 1_555 B DG 7 N2 ? ? A DG 7 B DG 107 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog15 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DA 8 N7 ? ? A DA 8 B DA 108 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog16 hydrog ? ? A DA 8 N7 ? ? ? 1_555 B DA 8 N6 ? ? A DA 8 B DA 108 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog17 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DC 9 O2 ? ? A DC 9 B DC 109 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DC 9 N4 ? ? A DC 9 B DC 109 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1NP5 _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 1NP5 _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 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DC 9 9 9 DC C A . n B 1 1 DG 1 101 101 DG G B . n B 1 2 DA 2 102 102 DA A B . n B 1 3 DC 3 103 103 DC C B . n B 1 4 DG 4 104 104 DG G B . n B 1 5 DA 5 105 105 DA A B . n B 1 6 DC 6 106 106 DC C B . n B 1 7 DG 7 107 107 DG G B . n B 1 8 DA 8 108 108 DA A B . n B 1 9 DC 9 109 109 DC C B . n # _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 2003-02-11 2 'Structure model' 1 1 2008-04-29 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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # 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_nmr_software 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_nmr_software.name' # 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 OP1 A DA 2 ? ? H21 B DG 101 ? ? 1.48 2 1 H21 A DG 1 ? ? OP1 B DA 102 ? ? 1.48 3 1 "H2'" A DA 8 ? ? "O4'" A DC 9 ? ? 1.54 4 1 "H2'" B DA 108 ? ? "O4'" B DC 109 ? ? 1.54 # 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 ? ? 111.02 108.30 2.72 0.30 N 2 1 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 117.74 113.10 4.64 0.50 N 3 1 C8 A DG 1 ? ? N9 A DG 1 ? ? C4 A DG 1 ? ? 103.42 106.40 -2.98 0.40 N 4 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 112.61 108.30 4.31 0.30 N 5 1 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 117.93 113.80 4.13 0.50 N 6 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 110.62 108.30 2.32 0.30 N 7 1 N7 A DG 4 ? ? C8 A DG 4 ? ? N9 A DG 4 ? ? 117.87 113.10 4.77 0.50 N 8 1 C8 A DG 4 ? ? N9 A DG 4 ? ? C4 A DG 4 ? ? 103.86 106.40 -2.54 0.40 N 9 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 111.49 108.30 3.19 0.30 N 10 1 N7 A DA 5 ? ? C8 A DA 5 ? ? N9 A DA 5 ? ? 117.73 113.80 3.93 0.50 N 11 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.83 108.30 2.53 0.30 N 12 1 N7 A DG 7 ? ? C8 A DG 7 ? ? N9 A DG 7 ? ? 117.94 113.10 4.84 0.50 N 13 1 C8 A DG 7 ? ? N9 A DG 7 ? ? C4 A DG 7 ? ? 103.91 106.40 -2.49 0.40 N 14 1 N7 A DA 8 ? ? C8 A DA 8 ? ? N9 A DA 8 ? ? 117.53 113.80 3.73 0.50 N 15 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 111.15 108.30 2.85 0.30 N 16 1 "O4'" B DG 101 ? ? "C1'" B DG 101 ? ? N9 B DG 101 ? ? 111.06 108.30 2.76 0.30 N 17 1 N7 B DG 101 ? ? C8 B DG 101 ? ? N9 B DG 101 ? ? 117.79 113.10 4.69 0.50 N 18 1 C8 B DG 101 ? ? N9 B DG 101 ? ? C4 B DG 101 ? ? 103.37 106.40 -3.03 0.40 N 19 1 "O4'" B DA 102 ? ? "C1'" B DA 102 ? ? N9 B DA 102 ? ? 112.58 108.30 4.28 0.30 N 20 1 N7 B DA 102 ? ? C8 B DA 102 ? ? N9 B DA 102 ? ? 117.89 113.80 4.09 0.50 N 21 1 "O4'" B DC 103 ? ? "C1'" B DC 103 ? ? N1 B DC 103 ? ? 110.37 108.30 2.07 0.30 N 22 1 "O4'" B DG 104 ? ? "C1'" B DG 104 ? ? N9 B DG 104 ? ? 110.63 108.30 2.33 0.30 N 23 1 N7 B DG 104 ? ? C8 B DG 104 ? ? N9 B DG 104 ? ? 117.83 113.10 4.73 0.50 N 24 1 C8 B DG 104 ? ? N9 B DG 104 ? ? C4 B DG 104 ? ? 103.88 106.40 -2.52 0.40 N 25 1 "O4'" B DA 105 ? ? "C1'" B DA 105 ? ? N9 B DA 105 ? ? 111.48 108.30 3.18 0.30 N 26 1 N7 B DA 105 ? ? C8 B DA 105 ? ? N9 B DA 105 ? ? 117.77 113.80 3.97 0.50 N 27 1 "O4'" B DG 107 ? ? "C1'" B DG 107 ? ? N9 B DG 107 ? ? 110.76 108.30 2.46 0.30 N 28 1 N7 B DG 107 ? ? C8 B DG 107 ? ? N9 B DG 107 ? ? 117.94 113.10 4.84 0.50 N 29 1 C8 B DG 107 ? ? N9 B DG 107 ? ? C4 B DG 107 ? ? 103.93 106.40 -2.47 0.40 N 30 1 N7 B DA 108 ? ? C8 B DA 108 ? ? N9 B DA 108 ? ? 117.48 113.80 3.68 0.50 N 31 1 "O4'" B DC 109 ? ? "C1'" B DC 109 ? ? N1 B DC 109 ? ? 111.32 108.30 3.02 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 1 DA A 2 ? ? 0.071 'SIDE CHAIN' 2 1 DA A 5 ? ? 0.055 'SIDE CHAIN' 3 1 DA B 102 ? ? 0.071 'SIDE CHAIN' 4 1 DA B 105 ? ? 0.055 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NP5 'double helix' 1NP5 'parallel strands' 1NP5 '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 1 1_555 B DG 1 1_555 -3.205 -7.847 -0.001 -22.889 -19.562 -179.998 1 A_DG1:DG101_B A 1 ? B 101 ? 4 12 1 A DA 2 1_555 B DA 2 1_555 -7.098 4.087 0.001 -7.337 19.030 -179.993 2 A_DA2:DA102_B A 2 ? B 102 ? 2 8 1 A DC 3 1_555 B DC 3 1_555 1.888 2.009 0.000 7.250 22.036 179.996 3 A_DC3:DC103_B A 3 ? B 103 ? 15 2 1 A DG 4 1_555 B DG 4 1_555 -3.486 -7.631 0.000 7.680 -38.789 -179.999 4 A_DG4:DG104_B A 4 ? B 104 ? 4 12 1 A DA 5 1_555 B DA 5 1_555 -6.298 4.673 0.000 -12.959 24.679 -179.998 5 A_DA5:DA105_B A 5 ? B 105 ? 2 8 1 A DC 6 1_555 B DC 6 1_555 -2.040 -1.544 0.000 -0.065 -7.635 -179.996 6 A_DC6:DC106_B A 6 ? B 106 ? 15 2 1 A DG 7 1_555 B DG 7 1_555 3.370 7.490 0.000 -24.869 37.158 179.996 7 A_DG7:DG107_B A 7 ? B 107 ? 4 12 1 A DA 8 1_555 B DA 8 1_555 5.909 -4.869 0.000 32.920 -32.699 180.000 8 A_DA8:DA108_B A 8 ? B 108 ? 2 7 1 A DC 9 1_555 B DC 9 1_555 -1.573 -1.527 0.000 4.240 32.862 -179.986 9 A_DC9:DC109_B A 9 ? B 109 ? 15 2 # 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 DG 1 1_555 A DA 2 1_555 B DA 2 1_555 0.000 -0.001 3.977 0.000 0.002 -1.385 -0.208 -0.022 3.977 -0.082 -0.011 -1.385 1 AA_DG1DA2:DA102DG101_BB A 1 ? B 101 ? A 2 ? B 102 ? 1 A DA 2 1_555 B DA 2 1_555 A DC 3 1_555 B DC 3 1_555 0.000 0.000 2.416 0.004 0.023 -108.394 0.000 0.000 2.416 -0.014 0.003 -108.394 2 AA_DA2DC3:DC103DA102_BB A 2 ? B 102 ? A 3 ? B 103 ? 1 A DC 3 1_555 B DC 3 1_555 A DG 4 1_555 B DG 4 1_555 0.000 -0.001 3.384 0.014 0.004 -118.820 0.000 0.000 3.384 -0.002 0.008 -118.820 3 AA_DC3DG4:DG104DC103_BB A 3 ? B 103 ? A 4 ? B 104 ? 1 A DG 4 1_555 B DG 4 1_555 A DA 5 1_555 B DA 5 1_555 0.000 0.000 4.819 0.001 0.003 -8.935 -0.012 0.004 4.819 -0.022 0.004 -8.935 4 AA_DG4DA5:DA105DG104_BB A 4 ? B 104 ? A 5 ? B 105 ? 1 A DA 5 1_555 B DA 5 1_555 A DC 6 1_555 B DC 6 1_555 0.000 0.000 2.694 0.008 -0.007 69.618 0.000 0.000 2.694 -0.006 -0.007 69.618 5 AA_DA5DC6:DC106DA105_BB A 5 ? B 105 ? A 6 ? B 106 ? 1 A DC 6 1_555 B DC 6 1_555 A DG 7 1_555 B DG 7 1_555 0.000 0.000 2.852 -0.008 0.005 -117.530 0.000 0.000 2.852 -0.003 -0.005 -117.530 6 AA_DC6DG7:DG107DC106_BB A 6 ? B 106 ? A 7 ? B 107 ? 1 A DG 7 1_555 B DG 7 1_555 A DA 8 1_555 B DA 8 1_555 0.000 0.000 4.968 0.005 -0.005 -10.452 0.012 0.011 4.968 0.027 0.025 -10.452 7 AA_DG7DA8:DA108DG107_BB A 7 ? B 107 ? A 8 ? B 108 ? 1 A DA 8 1_555 B DA 8 1_555 A DC 9 1_555 B DC 9 1_555 0.000 0.000 3.131 -0.006 0.006 -111.290 0.000 0.000 3.131 -0.003 -0.003 -111.290 8 AA_DA8DC9:DC109DA108_BB A 8 ? B 108 ? A 9 ? B 109 ? #