data_2A5P # _entry.id 2A5P # _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 2A5P pdb_00002a5p 10.2210/pdb2a5p/pdb RCSB RCSB033519 ? ? WWPDB D_1000033519 ? ? # 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 2005-07-26 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 5 'Structure model' 1 4 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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 5 'Structure model' chem_comp_atom 7 5 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2A5P _pdbx_database_status.recvd_initial_deposition_date 2005-06-30 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1EEG 'A(GGGG)A HEXAD' unspecified PDB 1JJP ;A(GGGG) PENTAD, 5' 3+1 tetrad ; unspecified PDB 1Y8D ;A(GGGG) PENTAD, 5' 3+1 tetrad ; unspecified PDB 1D6D 'AAT TRIAD IN DIAGONAL LOOP' unspecified PDB 2A5R . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Phan, A.T.' 1 'Kuryavyi, V.V.' 2 'Gaw, H.Y.' 3 'Patel, D.J.' 4 # _citation.id primary _citation.title 'Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.' _citation.journal_abbrev Nat.Chem.Biol. _citation.journal_volume 1 _citation.page_first 167 _citation.page_last 173 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1552-4450 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16408022 _citation.pdbx_database_id_DOI 10.1038/nchembio723 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Phan, A.T.' 1 ? primary 'Kuryavyi, V.' 2 ? primary 'Gaw, H.Y.' 3 ? primary 'Patel, D.J.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description "5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'" _entity.formula_weight 7701.934 _entity.pdbx_number_of_molecules 1 _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 ;(DT)(DG)(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DI)(DG)(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA)(DA)(DG)(DG) ; _entity_poly.pdbx_seq_one_letter_code_can TGAGGGTGGIGAGGGTGGGGAAGG _entity_poly.pdbx_strand_id A _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 DT n 1 2 DG n 1 3 DA n 1 4 DG n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DG n 1 9 DG n 1 10 DI n 1 11 DG n 1 12 DA n 1 13 DG n 1 14 DG n 1 15 DG n 1 16 DT n 1 17 DG n 1 18 DG n 1 19 DG n 1 20 DG n 1 21 DA n 1 22 DA n 1 23 DG n 1 24 DG n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name human _entity_src_nat.pdbx_organism_scientific 'Homo sapiens' _entity_src_nat.pdbx_ncbi_taxonomy_id 9606 _entity_src_nat.genus Homo _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details 'c-MYC gene' # 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 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DT 1 1 1 DT T A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DI 10 10 10 DI I A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DA 12 12 12 DA A A . n A 1 13 DG 13 13 13 DG G A . n A 1 14 DG 14 14 14 DG G A . n A 1 15 DG 15 15 15 DG G A . n A 1 16 DT 16 16 16 DT T A . n A 1 17 DG 17 17 17 DG G A . n A 1 18 DG 18 18 18 DG G A . n A 1 19 DG 19 19 19 DG G A . n A 1 20 DG 20 20 20 DG G A . n A 1 21 DA 21 21 21 DA A A . n A 1 22 DA 22 22 22 DA A A . n A 1 23 DG 23 23 23 DG G A . n A 1 24 DG 24 24 24 DG G A . n # _cell.entry_id 2A5P _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 2A5P _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2A5P _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 # _database_PDB_matrix.entry_id 2A5P _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 # _struct.entry_id 2A5P _struct.title ;Monomeric parallel-stranded DNA tetraplex with snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, NMR, 8 struct. ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2A5P _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;MONOMERIC PARALLEL-STRANDED QUADRUPLEX; C-MYC PROMOTER 3+1 G-TETRAD; SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP; GAG TRIAD; GAAG LOOP, DNA ; # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2A5P _struct_ref.pdbx_db_accession 2A5P _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2A5P _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 24 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2A5P _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 24 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 # 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 DA 3 N1 ? ? ? 1_555 A DA 12 N6 ? ? A DA 3 A DA 12 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog2 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DA 12 N1 ? ? A DA 3 A DA 12 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog3 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 8 O6 ? ? A DG 4 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 8 N7 ? ? A DG 4 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 4 N7 ? ? ? 1_555 A DG 17 N2 ? ? A DG 4 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DG 17 N1 ? ? A DG 4 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 5 N1 ? ? ? 1_555 A DG 9 O6 ? ? A DG 5 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 5 N2 ? ? ? 1_555 A DG 9 N7 ? ? A DG 5 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 5 N7 ? ? ? 1_555 A DG 18 N2 ? ? A DG 5 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 5 O6 ? ? ? 1_555 A DG 18 N1 ? ? A DG 5 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 6 N7 ? ? ? 1_555 A DG 19 N2 ? ? A DG 6 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DG 19 N1 ? ? A DG 6 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DG 24 O6 ? ? A DG 6 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DG 24 N7 ? ? A DG 6 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DG 13 O6 ? ? A DG 8 A DG 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DG 13 N7 ? ? A DG 8 A DG 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DG 14 O6 ? ? A DG 9 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DG 14 N7 ? ? A DG 9 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DG 13 N1 ? ? ? 1_555 A DG 17 O6 ? ? A DG 13 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A DG 13 N2 ? ? ? 1_555 A DG 17 N7 ? ? A DG 13 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? A DG 14 N1 ? ? ? 1_555 A DG 18 O6 ? ? A DG 14 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A DG 14 N2 ? ? ? 1_555 A DG 18 N7 ? ? A DG 14 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? A DG 15 N1 ? ? ? 1_555 A DG 19 O6 ? ? A DG 15 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? A DG 15 N2 ? ? ? 1_555 A DG 19 N7 ? ? A DG 15 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? A DG 15 N7 ? ? ? 1_555 A DG 24 N2 ? ? A DG 15 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? A DG 15 O6 ? ? ? 1_555 A DG 24 N1 ? ? A DG 15 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? A DG 20 N2 ? ? ? 1_555 A DA 22 N7 ? ? A DG 20 A DA 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog28 hydrog ? ? A DG 20 N3 ? ? ? 1_555 A DA 22 N6 ? ? A DG 20 A DA 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog29 hydrog ? ? A DG 20 N1 ? ? ? 1_555 A DG 23 O6 ? ? A DG 20 A DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? A DG 20 N2 ? ? ? 1_555 A DG 23 N7 ? ? A DG 20 A DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.558 1.512 0.046 0.007 N 2 1 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.565 1.512 0.053 0.007 N 3 1 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.570 1.512 0.058 0.007 N 4 2 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.563 1.512 0.051 0.007 N 5 2 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.567 1.512 0.055 0.007 N 6 2 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.564 1.512 0.052 0.007 N 7 2 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.564 1.512 0.052 0.007 N 8 3 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.559 1.512 0.047 0.007 N 9 3 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.565 1.512 0.053 0.007 N 10 3 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.568 1.512 0.056 0.007 N 11 4 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.565 1.512 0.053 0.007 N 12 4 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.565 1.512 0.053 0.007 N 13 4 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.562 1.512 0.050 0.007 N 14 4 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.567 1.512 0.055 0.007 N 15 5 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.556 1.512 0.044 0.007 N 16 5 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.555 1.512 0.043 0.007 N 17 5 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.563 1.512 0.051 0.007 N 18 5 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.570 1.512 0.058 0.007 N 19 6 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.557 1.512 0.045 0.007 N 20 6 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.558 1.512 0.046 0.007 N 21 6 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.566 1.512 0.054 0.007 N 22 6 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.570 1.512 0.058 0.007 N 23 7 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.555 1.512 0.043 0.007 N 24 7 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.555 1.512 0.043 0.007 N 25 7 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.562 1.512 0.050 0.007 N 26 7 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.562 1.512 0.050 0.007 N 27 8 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.557 1.512 0.045 0.007 N 28 8 "C5'" A DG 20 ? ? "C4'" A DG 20 ? ? 1.563 1.512 0.051 0.007 N 29 8 "C5'" A DG 23 ? ? "C4'" A DG 23 ? ? 1.566 1.512 0.054 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.88 108.30 2.58 0.30 N 2 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.29 108.30 1.99 0.30 N 3 1 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.61 108.30 3.31 0.30 N 4 1 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 110.87 108.30 2.57 0.30 N 5 1 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 111.68 108.30 3.38 0.30 N 6 1 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.30 108.30 2.00 0.30 N 7 1 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 110.66 108.30 2.36 0.30 N 8 1 "O4'" A DG 23 ? ? "C1'" A DG 23 ? ? N9 A DG 23 ? ? 110.19 108.30 1.89 0.30 N 9 2 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.19 108.30 1.89 0.30 N 10 2 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 110.41 108.30 2.11 0.30 N 11 2 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.00 108.30 2.70 0.30 N 12 2 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 110.38 108.30 2.08 0.30 N 13 2 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 112.01 108.30 3.71 0.30 N 14 2 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.62 108.30 2.32 0.30 N 15 2 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 111.14 108.30 2.84 0.30 N 16 3 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.63 108.30 2.33 0.30 N 17 3 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.32 108.30 2.02 0.30 N 18 3 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 112.80 108.30 4.50 0.30 N 19 3 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.97 108.30 3.67 0.30 N 20 3 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 111.05 108.30 2.75 0.30 N 21 3 "O4'" A DT 16 ? ? "C1'" A DT 16 ? ? N1 A DT 16 ? ? 110.24 108.30 1.94 0.30 N 22 3 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 112.02 108.30 3.72 0.30 N 23 3 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.44 108.30 2.14 0.30 N 24 3 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 110.86 108.30 2.56 0.30 N 25 3 "O4'" A DG 23 ? ? "C1'" A DG 23 ? ? N9 A DG 23 ? ? 110.24 108.30 1.94 0.30 N 26 4 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.46 108.30 2.16 0.30 N 27 4 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.83 108.30 2.53 0.30 N 28 4 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.19 108.30 1.89 0.30 N 29 4 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 111.18 108.30 2.88 0.30 N 30 4 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.99 108.30 3.69 0.30 N 31 4 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 111.56 108.30 3.26 0.30 N 32 4 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 110.98 108.30 2.68 0.30 N 33 4 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.39 108.30 2.09 0.30 N 34 4 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 110.95 108.30 2.65 0.30 N 35 4 "O4'" A DG 23 ? ? "C1'" A DG 23 ? ? N9 A DG 23 ? ? 110.21 108.30 1.91 0.30 N 36 5 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.67 108.30 2.37 0.30 N 37 5 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.70 108.30 2.40 0.30 N 38 5 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? "C1'" A DG 6 ? ? 97.37 102.40 -5.03 0.80 N 39 5 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 110.25 108.30 1.95 0.30 N 40 5 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 110.38 108.30 2.08 0.30 N 41 5 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 111.23 108.30 2.93 0.30 N 42 5 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.47 108.30 2.17 0.30 N 43 5 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 110.66 108.30 2.36 0.30 N 44 5 "O4'" A DG 23 ? ? "C1'" A DG 23 ? ? N9 A DG 23 ? ? 110.12 108.30 1.82 0.30 N 45 6 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.29 108.30 1.99 0.30 N 46 6 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.42 108.30 2.12 0.30 N 47 6 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.85 108.30 2.55 0.30 N 48 6 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 110.68 108.30 2.38 0.30 N 49 6 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 110.28 108.30 1.98 0.30 N 50 6 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 110.80 108.30 2.50 0.30 N 51 6 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.52 108.30 2.22 0.30 N 52 6 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 111.03 108.30 2.73 0.30 N 53 6 "O4'" A DG 23 ? ? "C1'" A DG 23 ? ? N9 A DG 23 ? ? 110.10 108.30 1.80 0.30 N 54 7 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.46 108.30 2.16 0.30 N 55 7 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.61 108.30 2.31 0.30 N 56 7 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.35 108.30 2.05 0.30 N 57 7 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.29 108.30 2.99 0.30 N 58 7 "O4'" A DT 16 ? ? "C1'" A DT 16 ? ? N1 A DT 16 ? ? 110.23 108.30 1.93 0.30 N 59 7 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 111.15 108.30 2.85 0.30 N 60 7 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.76 108.30 2.46 0.30 N 61 7 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 111.16 108.30 2.86 0.30 N 62 8 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.57 108.30 2.27 0.30 N 63 8 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.63 108.30 2.33 0.30 N 64 8 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 113.49 108.30 5.19 0.30 N 65 8 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 113.15 108.30 4.85 0.30 N 66 8 "O4'" A DG 17 ? ? "C1'" A DG 17 ? ? N9 A DG 17 ? ? 111.84 108.30 3.54 0.30 N 67 8 "O4'" A DG 19 ? ? "C1'" A DG 19 ? ? N9 A DG 19 ? ? 110.42 108.30 2.12 0.30 N 68 8 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 111.26 108.30 2.96 0.30 N # _pdbx_nmr_ensemble.entry_id 2A5P _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _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 2A5P _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '70 MM KCL 20 MM POTASSIUM PHOSPHATE, 100% D2O' '100% D2O' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength '90 mM' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '1H-1H NOESY' 1 2 1 '1H-1H TOCSY' 1 3 1 '1H-31P COSY' 1 4 1 '1H-1H COSY' 1 5 1 '1H-15N JRHMQC' 1 6 1 '1H-15N HMBC' 1 7 1 '1H-13C JRHM 1H-13C HMBC' 1 8 1 '1H-13C HSQC' 1 9 1 '1H-13C sHMBC' 1 10 1 '1H-31P TOCSY' 1 # _pdbx_nmr_details.entry_id 2A5P _pdbx_nmr_details.text ;A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY TERMS WERE FURTHER OPTIMIZED WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE PROPORTION 1:4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE THEN SLOWLY COOLED TO 300K IN 14 PS AND EQUILIBRATED AT 300K FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES OF NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 to 16. AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-2). ; # _pdbx_nmr_refine.entry_id 2A5P _pdbx_nmr_refine.method ;DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENT ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement XPLOR 3.851 'AT BRUNGER' 1 collection VNMR 6.0 VARIAN 2 processing Felix 2000 ACCELRYS 3 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DG OP3 O N N 37 DG P P N N 38 DG OP1 O N N 39 DG OP2 O N N 40 DG "O5'" O N N 41 DG "C5'" C N N 42 DG "C4'" C N R 43 DG "O4'" O N N 44 DG "C3'" C N S 45 DG "O3'" O N N 46 DG "C2'" C N N 47 DG "C1'" C N R 48 DG N9 N Y N 49 DG C8 C Y N 50 DG N7 N Y N 51 DG C5 C Y N 52 DG C6 C N N 53 DG O6 O N N 54 DG N1 N N N 55 DG C2 C N N 56 DG N2 N N N 57 DG N3 N N N 58 DG C4 C Y N 59 DG HOP3 H N N 60 DG HOP2 H N N 61 DG "H5'" H N N 62 DG "H5''" H N N 63 DG "H4'" H N N 64 DG "H3'" H N N 65 DG "HO3'" H N N 66 DG "H2'" H N N 67 DG "H2''" H N N 68 DG "H1'" H N N 69 DG H8 H N N 70 DG H1 H N N 71 DG H21 H N N 72 DG H22 H N N 73 DI OP3 O N N 74 DI P P N N 75 DI OP1 O N N 76 DI OP2 O N N 77 DI "O5'" O N N 78 DI "C5'" C N N 79 DI "C4'" C N R 80 DI "O4'" O N N 81 DI "C3'" C N S 82 DI "O3'" O N N 83 DI "C2'" C N N 84 DI "C1'" C N R 85 DI N9 N Y N 86 DI C8 C Y N 87 DI N7 N Y N 88 DI C5 C Y N 89 DI C6 C N N 90 DI O6 O N N 91 DI N1 N N N 92 DI C2 C N N 93 DI N3 N N N 94 DI C4 C Y N 95 DI HOP3 H N N 96 DI HOP2 H N N 97 DI "H5'" H N N 98 DI "H5''" H N N 99 DI "H4'" H N N 100 DI "H3'" H N N 101 DI "HO3'" H N N 102 DI "H2'" H N N 103 DI "H2''" H N N 104 DI "H1'" H N N 105 DI H8 H N N 106 DI H1 H N N 107 DI H2 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DG OP3 P sing N N 39 DG OP3 HOP3 sing N N 40 DG P OP1 doub N N 41 DG P OP2 sing N N 42 DG P "O5'" sing N N 43 DG OP2 HOP2 sing N N 44 DG "O5'" "C5'" sing N N 45 DG "C5'" "C4'" sing N N 46 DG "C5'" "H5'" sing N N 47 DG "C5'" "H5''" sing N N 48 DG "C4'" "O4'" sing N N 49 DG "C4'" "C3'" sing N N 50 DG "C4'" "H4'" sing N N 51 DG "O4'" "C1'" sing N N 52 DG "C3'" "O3'" sing N N 53 DG "C3'" "C2'" sing N N 54 DG "C3'" "H3'" sing N N 55 DG "O3'" "HO3'" sing N N 56 DG "C2'" "C1'" sing N N 57 DG "C2'" "H2'" sing N N 58 DG "C2'" "H2''" sing N N 59 DG "C1'" N9 sing N N 60 DG "C1'" "H1'" sing N N 61 DG N9 C8 sing Y N 62 DG N9 C4 sing Y N 63 DG C8 N7 doub Y N 64 DG C8 H8 sing N N 65 DG N7 C5 sing Y N 66 DG C5 C6 sing N N 67 DG C5 C4 doub Y N 68 DG C6 O6 doub N N 69 DG C6 N1 sing N N 70 DG N1 C2 sing N N 71 DG N1 H1 sing N N 72 DG C2 N2 sing N N 73 DG C2 N3 doub N N 74 DG N2 H21 sing N N 75 DG N2 H22 sing N N 76 DG N3 C4 sing N N 77 DI OP3 P sing N N 78 DI OP3 HOP3 sing N N 79 DI P OP1 doub N N 80 DI P OP2 sing N N 81 DI P "O5'" sing N N 82 DI OP2 HOP2 sing N N 83 DI "O5'" "C5'" sing N N 84 DI "C5'" "C4'" sing N N 85 DI "C5'" "H5'" sing N N 86 DI "C5'" "H5''" sing N N 87 DI "C4'" "O4'" sing N N 88 DI "C4'" "C3'" sing N N 89 DI "C4'" "H4'" sing N N 90 DI "O4'" "C1'" sing N N 91 DI "C3'" "O3'" sing N N 92 DI "C3'" "C2'" sing N N 93 DI "C3'" "H3'" sing N N 94 DI "O3'" "HO3'" sing N N 95 DI "C2'" "C1'" sing N N 96 DI "C2'" "H2'" sing N N 97 DI "C2'" "H2''" sing N N 98 DI "C1'" N9 sing N N 99 DI "C1'" "H1'" sing N N 100 DI N9 C8 sing Y N 101 DI N9 C4 sing Y N 102 DI C8 N7 doub Y N 103 DI C8 H8 sing N N 104 DI N7 C5 sing Y N 105 DI C5 C6 sing N N 106 DI C5 C4 doub Y N 107 DI C6 O6 doub N N 108 DI C6 N1 sing N N 109 DI N1 C2 sing N N 110 DI N1 H1 sing N N 111 DI C2 N3 doub N N 112 DI C2 H2 sing N N 113 DI N3 C4 sing N N 114 DT OP3 P sing N N 115 DT OP3 HOP3 sing N N 116 DT P OP1 doub N N 117 DT P OP2 sing N N 118 DT P "O5'" sing N N 119 DT OP2 HOP2 sing N N 120 DT "O5'" "C5'" sing N N 121 DT "C5'" "C4'" sing N N 122 DT "C5'" "H5'" sing N N 123 DT "C5'" "H5''" sing N N 124 DT "C4'" "O4'" sing N N 125 DT "C4'" "C3'" sing N N 126 DT "C4'" "H4'" sing N N 127 DT "O4'" "C1'" sing N N 128 DT "C3'" "O3'" sing N N 129 DT "C3'" "C2'" sing N N 130 DT "C3'" "H3'" sing N N 131 DT "O3'" "HO3'" sing N N 132 DT "C2'" "C1'" sing N N 133 DT "C2'" "H2'" sing N N 134 DT "C2'" "H2''" sing N N 135 DT "C1'" N1 sing N N 136 DT "C1'" "H1'" sing N N 137 DT N1 C2 sing N N 138 DT N1 C6 sing N N 139 DT C2 O2 doub N N 140 DT C2 N3 sing N N 141 DT N3 C4 sing N N 142 DT N3 H3 sing N N 143 DT C4 O4 doub N N 144 DT C4 C5 sing N N 145 DT C5 C7 sing N N 146 DT C5 C6 doub N N 147 DT C7 H71 sing N N 148 DT C7 H72 sing N N 149 DT C7 H73 sing N N 150 DT C6 H6 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2A5P 'double helix' 2A5P 'quadruple 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 DA 3 1_555 A DA 12 1_555 -1.653 -0.678 0.074 11.584 8.994 172.530 1 A_DA3:DA12_A A 3 ? A 12 ? 1 2 1 A DG 8 1_555 A DG 13 1_555 1.655 3.502 -0.114 4.578 -3.560 -91.960 2 A_DG8:DG13_A A 8 ? A 13 ? 6 ? 1 A DG 4 1_555 A DG 17 1_555 -1.602 -3.381 -0.085 7.759 -2.843 93.661 3 A_DG4:DG17_A A 4 ? A 17 ? 6 ? 1 A DG 5 1_555 A DG 18 1_555 -1.146 -3.793 0.113 7.187 -8.519 89.175 4 A_DG5:DG18_A A 5 ? A 18 ? 6 ? 1 A DG 15 1_555 A DG 19 1_555 1.370 3.823 0.043 -2.995 1.589 -87.670 5 A_DG15:DG19_A A 15 ? A 19 ? 6 ? 1 A DG 24 1_555 A DG 6 1_555 -1.100 -3.672 -0.121 5.687 0.256 93.509 6 A_DG24:DG6_A A 24 ? A 6 ? 6 ? 1 A DG 9 1_555 A DG 14 1_555 1.013 3.750 -0.178 0.523 0.115 -93.541 7 A_DG9:DG14_A A 9 ? A 14 ? 6 ? 1 A DG 20 1_555 A DG 23 1_555 1.757 3.591 -0.008 11.115 -11.150 -89.991 8 A_DG20:DG23_A A 20 ? A 23 ? 6 ? # 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 DA 3 1_555 A DA 12 1_555 A DG 8 1_555 A DG 13 1_555 -1.261 1.378 3.203 3.194 -5.700 -118.767 -0.745 -0.701 3.263 3.310 1.855 -118.877 1 AA_DA3DG8:DG13DA12_AA A 3 ? A 12 ? A 8 ? A 13 ? 1 A DG 8 1_555 A DG 13 1_555 A DG 4 1_555 A DG 17 1_555 1.850 3.658 0.261 3.943 -4.161 -179.420 -1.829 0.925 0.261 2.081 1.971 -179.421 2 AA_DG8DG4:DG17DG13_AA A 8 ? A 13 ? A 4 ? A 17 ? 1 A DG 4 1_555 A DG 17 1_555 A DG 5 1_555 A DG 18 1_555 -0.329 -1.124 3.460 -1.385 -4.878 30.675 -1.082 0.325 3.602 -9.142 2.595 31.081 3 AA_DG4DG5:DG18DG17_AA A 4 ? A 17 ? A 5 ? A 18 ? 1 A DG 5 1_555 A DG 18 1_555 A DG 15 1_555 A DG 19 1_555 0.360 2.083 3.007 -2.562 5.768 -60.159 -2.320 0.246 2.827 -5.737 -2.549 -60.459 4 AA_DG5DG15:DG19DG18_AA A 5 ? A 18 ? A 15 ? A 19 ? 1 A DG 15 1_555 A DG 19 1_555 A DG 24 1_555 A DG 6 1_555 -1.365 -3.747 0.047 -1.492 0.987 178.534 -1.873 0.682 0.046 0.494 0.746 178.534 5 AA_DG15DG24:DG6DG19_AA A 15 ? A 19 ? A 24 ? A 6 ? 1 A DG 24 1_555 A DG 6 1_555 A DG 9 1_555 A DG 14 1_555 -1.167 -1.806 -3.208 0.633 -0.674 60.977 -1.811 1.121 -3.201 -0.664 -0.624 60.984 6 AA_DG24DG9:DG14DG6_AA A 24 ? A 6 ? A 9 ? A 14 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 'VARIAN UNITY INOVA' Varian 600 ? 2 AVANCE Bruker 800 ? # _atom_sites.entry_id 2A5P _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_