data_2KH4 # _entry.id 2KH4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2KH4 pdb_00002kh4 10.2210/pdb2kh4/pdb RCSB RCSB101113 ? ? WWPDB D_1000101113 ? ? BMRB 16223 ? 10.13018/BMR16223 # 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 2009-12-15 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-02-26 4 'Structure model' 1 3 2024-05-01 # _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 3 'Structure model' Other 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' # 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_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' struct_conn 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 # 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' '_pdbx_database_status.status_code_cs' 2 3 'Structure model' '_pdbx_nmr_software.name' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' # _database_PDB_caveat.id 1 _database_PDB_caveat.text ;Chirality error at C1' center of FAG in Chain A ; # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KH4 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-03-24 _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.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2KH3 unspecified . BMRB 16223 unspecified . # _audit_author.name 'Brown, K.L.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 131 _citation.page_first 16096 _citation.page_last 16107 _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 19831353 _citation.pdbx_database_id_DOI 10.1021/ja902052v # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Brown, K.L.' 1 ? primary 'Voehler, M.W.' 2 ? primary 'Magee, S.M.' 3 ? primary 'Harris, C.M.' 4 ? primary 'Harris, T.M.' 5 ? primary 'Stone, M.P.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*CP*TP*(FAG)P*A)-3'" _entity.formula_weight 1537.118 _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 yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DT)(FAG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can CTNA _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 DC n 1 2 DT n 1 3 FAG n 1 4 DA 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 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 FAG 'DNA linking' . ;[1',2'-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]-FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]-RIBOFURANOSE]-5-MONOPHOSPHATE GROUP ; ? 'C27 H28 N5 O15 P' 693.509 # 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 DC 1 1 1 DC DC A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 FAG 3 3 3 FAG FAG A . n A 1 4 DA 4 4 4 DA DA A . n # _cell.entry_id 2KH4 _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 2KH4 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _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 2KH4 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KH4 _struct.title 'Aflatoxin Formamidopyrimidine alpha anomer in single strand DNA' _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KH4 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Aflatoxin, Formamidopyrimidine, alpha anomer, 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.db_name PDB _struct_ref.db_code 2KH4 _struct_ref.pdbx_db_accession 2KH4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code CTXA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KH4 _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 4 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2KH4 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 4 _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 4 # _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 _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 DT 2 "O3'" ? ? ? 1_555 A FAG 3 P ? ? A DT 2 A FAG 3 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale one ? A FAG 3 "O3'" ? ? ? 1_555 A DA 4 P ? ? A FAG 3 A DA 4 1_555 ? ? ? ? ? ? ? 1.607 ? ? # _struct_conn_type.id covale _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 DC 1 ? ? C6 A DC 1 ? ? 1.426 1.339 0.087 0.008 N 2 1 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.430 1.339 0.091 0.007 N 3 1 P A DA 4 ? ? OP1 A DA 4 ? ? 1.383 1.485 -0.102 0.017 N 4 2 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.424 1.339 0.085 0.008 N 5 2 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.427 1.339 0.088 0.007 N 6 3 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? 0.970 1.418 -0.448 0.025 N 7 3 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 1.426 1.509 -0.083 0.011 N 8 3 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 1.436 1.516 -0.080 0.008 N 9 3 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.380 1.419 -0.039 0.006 N 10 3 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.425 1.339 0.086 0.008 N 11 3 "O3'" A DC 1 ? ? P A DT 2 ? ? 1.525 1.607 -0.082 0.012 Y 12 3 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.428 1.339 0.089 0.007 N 13 4 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.424 1.339 0.085 0.008 N 14 4 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.429 1.339 0.090 0.007 N 15 4 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? 1.401 1.516 -0.115 0.008 N 16 4 "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 1.439 1.518 -0.079 0.010 N 17 4 "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? 1.353 1.446 -0.093 0.010 N 18 4 "O3'" A DA 4 ? ? "C3'" A DA 4 ? ? 1.303 1.419 -0.116 0.006 N 19 5 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.426 1.339 0.087 0.008 N 20 5 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.428 1.339 0.089 0.007 N 21 5 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? 1.401 1.516 -0.115 0.008 N 22 5 "O3'" A DA 4 ? ? "C3'" A DA 4 ? ? 1.283 1.419 -0.136 0.006 N 23 6 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.426 1.339 0.087 0.008 N 24 6 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.428 1.339 0.089 0.007 N 25 7 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 1.448 1.516 -0.068 0.008 N 26 7 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.426 1.339 0.087 0.008 N 27 7 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.429 1.339 0.090 0.007 N 28 8 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.425 1.339 0.086 0.008 N 29 8 C5 A DT 2 ? ? C6 A DT 2 ? ? 1.429 1.339 0.090 0.007 N 30 8 P A DA 4 ? ? OP1 A DA 4 ? ? 1.340 1.485 -0.145 0.017 N 31 8 P A DA 4 ? ? OP2 A DA 4 ? ? 1.274 1.485 -0.211 0.017 N 32 8 P A DA 4 ? ? "O5'" A DA 4 ? ? 1.446 1.593 -0.147 0.010 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 DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 112.49 106.00 6.49 0.60 N 2 1 "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 96.07 102.20 -6.13 0.70 N 3 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 111.24 102.50 8.74 1.20 N 4 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.80 108.30 4.50 0.30 N 5 1 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 113.01 108.30 4.71 0.30 N 6 1 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.23 119.90 4.33 0.60 N 7 1 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.66 124.90 -4.24 0.70 N 8 1 "O5'" A DA 4 ? ? "C5'" A DA 4 ? ? "C4'" A DA 4 ? ? 103.47 109.40 -5.93 0.80 N 9 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? "C2'" A DA 4 ? ? 101.06 105.90 -4.84 0.80 N 10 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 114.51 108.30 6.21 0.30 N 11 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.41 108.30 2.11 0.30 N 12 2 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.88 108.30 4.58 0.30 N 13 2 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.40 119.90 4.50 0.60 N 14 2 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.53 124.90 -4.37 0.70 N 15 2 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.96 108.30 3.66 0.30 N 16 2 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.98 117.00 -3.02 0.50 N 17 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.36 108.30 3.06 0.30 N 18 3 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 113.10 108.30 4.80 0.30 N 19 3 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.31 119.90 4.41 0.60 N 20 3 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.59 124.90 -4.31 0.70 N 21 3 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 113.34 108.30 5.04 0.30 N 22 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.76 108.30 3.46 0.30 N 23 4 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.63 108.30 4.33 0.30 N 24 4 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.15 119.90 4.25 0.60 N 25 4 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.64 124.90 -4.26 0.70 N 26 4 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.96 108.30 4.66 0.30 N 27 5 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.12 108.30 2.82 0.30 N 28 5 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.82 108.30 4.52 0.30 N 29 5 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.25 119.90 4.35 0.60 N 30 5 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.66 124.90 -4.24 0.70 N 31 5 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.39 108.30 4.09 0.30 N 32 6 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.18 108.30 3.88 0.30 N 33 6 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.75 108.30 4.45 0.30 N 34 6 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.18 119.90 4.28 0.60 N 35 6 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.63 124.90 -4.27 0.70 N 36 6 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.89 108.30 3.59 0.30 N 37 7 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.53 108.30 4.23 0.30 N 38 7 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.26 108.30 3.96 0.30 N 39 7 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.28 119.90 4.38 0.60 N 40 7 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.54 124.90 -4.36 0.70 N 41 7 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 113.05 108.30 4.75 0.30 N 42 8 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 100.80 114.10 -13.30 1.80 N 43 8 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.63 108.30 4.33 0.30 N 44 8 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 112.70 108.30 4.40 0.30 N 45 8 N3 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 124.31 119.90 4.41 0.60 N 46 8 C5 A DT 2 ? ? C4 A DT 2 ? ? O4 A DT 2 ? ? 120.60 124.90 -4.30 0.70 N 47 8 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.17 108.30 3.87 0.30 N # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 "C1'" ? A FAG 3 ? 'WRONG HAND' . 2 2 "C1'" ? A FAG 3 ? 'WRONG HAND' . 3 3 "C1'" ? A FAG 3 ? 'WRONG HAND' . 4 4 "C1'" ? A FAG 3 ? 'WRONG HAND' . 5 5 "C1'" ? A FAG 3 ? 'WRONG HAND' . 6 6 "C1'" ? A FAG 3 ? 'WRONG HAND' . 7 7 "C1'" ? A FAG 3 ? 'WRONG HAND' . 8 8 "C1'" ? A FAG 3 ? 'WRONG HAND' . # _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 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.conformers_calculated_total_number 8 _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KH4 _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 2KH4 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.4 mM (5'-D(*DCP*DTP*(FAG)P*DA)-3')-1, 100% D2O ; 1 '100% D2O' ;0.4 mM (5'-D(*DCP*DTP*(FAG)P*DA)-3')-2, 90% H2O/10% D2O ; 2 '90% H2O/10% D2O' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id "5'-D(*DCP*DTP*(FAG)P*DA)-3'-1" 0.4 ? mM ? 1 "5'-D(*DCP*DTP*(FAG)P*DA)-3'-2" 0.4 ? mM ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.1 _pdbx_nmr_exptl_sample_conditions.pH 8.7 _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 COSY' 1 3 2 '2D 1H-1H NOESY' # _pdbx_nmr_refine.entry_id 2KH4 _pdbx_nmr_refine.method 'molecular 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 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' refinement Amber 9 1 Goddard 'chemical shift assignment' Sparky ? 2 Goddard 'data analysis' Sparky ? 3 'Bruker Biospin' processing TopSpin ? 4 'Borgias, B.A. & James, T.L.' 'restraint generation' MARDIGRAS ? 5 'James T.L.' 'structure validation' CORMA ? 6 'Lavery, R. and Sklenar, H' 'data analysis' Curves ? 7 # 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 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DT OP3 O N N 71 DT P P N N 72 DT OP1 O N N 73 DT OP2 O N N 74 DT "O5'" O N N 75 DT "C5'" C N N 76 DT "C4'" C N R 77 DT "O4'" O N N 78 DT "C3'" C N S 79 DT "O3'" O N N 80 DT "C2'" C N N 81 DT "C1'" C N R 82 DT N1 N N N 83 DT C2 C N N 84 DT O2 O N N 85 DT N3 N N N 86 DT C4 C N N 87 DT O4 O N N 88 DT C5 C N N 89 DT C7 C N N 90 DT C6 C N N 91 DT HOP3 H N N 92 DT HOP2 H N N 93 DT "H5'" H N N 94 DT "H5''" H N N 95 DT "H4'" H N N 96 DT "H3'" H N N 97 DT "HO3'" H N N 98 DT "H2'" H N N 99 DT "H2''" H N N 100 DT "H1'" H N N 101 DT H3 H N N 102 DT H71 H N N 103 DT H72 H N N 104 DT H73 H N N 105 DT H6 H N N 106 FAG C3A C N N 107 FAG C3 C N N 108 FAG C2A C N N 109 FAG C1 C N N 110 FAG O1 O N N 111 FAG P P N N 112 FAG O1P O N N 113 FAG O2P O N N 114 FAG "O5'" O N N 115 FAG "C5'" C N N 116 FAG "C4'" C N R 117 FAG "O4'" O N N 118 FAG "C1'" C N R 119 FAG N9 N N N 120 FAG C4 C N N 121 FAG N3 N N N 122 FAG C2 C N N 123 FAG N2 N N N 124 FAG N1 N N N 125 FAG C6 C N N 126 FAG O6 O N N 127 FAG C5 C N N 128 FAG N7 N N N 129 FAG C8 C N N 130 FAG O8 O N N 131 FAG "C2'" C N N 132 FAG "C3'" C N S 133 FAG "O3'" O N N 134 FAG C8A C N R 135 FAG C9 C N R 136 FAG O9 O N N 137 FAG C9A C N R 138 FAG C9B C Y N 139 FAG O7 O N N 140 FAG C6A C N S 141 FAG O6A O N N 142 FAG C5M C Y N 143 FAG C5B C Y N 144 FAG C4B C Y N 145 FAG O4 O N N 146 FAG CM C N N 147 FAG C4A C Y N 148 FAG CAA C Y N 149 FAG O10 O N N 150 FAG C11 C N N 151 FAG O11 O N N 152 FAG CBA C N N 153 FAG H31 H N N 154 FAG H32 H N N 155 FAG H2A1 H N N 156 FAG H2A2 H N N 157 FAG HOP2 H N N 158 FAG "H5'1" H N N 159 FAG "H5'2" H N N 160 FAG "H4'" H N N 161 FAG "H1'" H N N 162 FAG HN9 H N N 163 FAG HN21 H N N 164 FAG HN22 H N N 165 FAG H1 H N N 166 FAG H8 H N N 167 FAG "H2'1" H N N 168 FAG "H2'2" H N N 169 FAG "H3'" H N N 170 FAG "HO3'" H N N 171 FAG H8A H N N 172 FAG H9 H N N 173 FAG HO9 H N N 174 FAG H9A H N N 175 FAG H6A H N N 176 FAG H5B H N N 177 FAG HM1 H N N 178 FAG HM2 H N N 179 FAG HM3 H N N 180 FAG O3P O N N 181 FAG HOP3 H N N 182 # 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 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DT OP3 P sing N N 74 DT OP3 HOP3 sing N N 75 DT P OP1 doub N N 76 DT P OP2 sing N N 77 DT P "O5'" sing N N 78 DT OP2 HOP2 sing N N 79 DT "O5'" "C5'" sing N N 80 DT "C5'" "C4'" sing N N 81 DT "C5'" "H5'" sing N N 82 DT "C5'" "H5''" sing N N 83 DT "C4'" "O4'" sing N N 84 DT "C4'" "C3'" sing N N 85 DT "C4'" "H4'" sing N N 86 DT "O4'" "C1'" sing N N 87 DT "C3'" "O3'" sing N N 88 DT "C3'" "C2'" sing N N 89 DT "C3'" "H3'" sing N N 90 DT "O3'" "HO3'" sing N N 91 DT "C2'" "C1'" sing N N 92 DT "C2'" "H2'" sing N N 93 DT "C2'" "H2''" sing N N 94 DT "C1'" N1 sing N N 95 DT "C1'" "H1'" sing N N 96 DT N1 C2 sing N N 97 DT N1 C6 sing N N 98 DT C2 O2 doub N N 99 DT C2 N3 sing N N 100 DT N3 C4 sing N N 101 DT N3 H3 sing N N 102 DT C4 O4 doub N N 103 DT C4 C5 sing N N 104 DT C5 C7 sing N N 105 DT C5 C6 doub N N 106 DT C7 H71 sing N N 107 DT C7 H72 sing N N 108 DT C7 H73 sing N N 109 DT C6 H6 sing N N 110 FAG C3A C3 sing N N 111 FAG C3A C4A sing N N 112 FAG C3A CBA doub N N 113 FAG C3 C2A sing N N 114 FAG C3 H31 sing N N 115 FAG C3 H32 sing N N 116 FAG C2A C1 sing N N 117 FAG C2A H2A1 sing N N 118 FAG C2A H2A2 sing N N 119 FAG C1 O1 doub N N 120 FAG C1 CBA sing N N 121 FAG P O1P doub N N 122 FAG P O2P sing N N 123 FAG P "O5'" sing N N 124 FAG O2P HOP2 sing N N 125 FAG "O5'" "C5'" sing N N 126 FAG "C5'" "C4'" sing N N 127 FAG "C5'" "H5'1" sing N N 128 FAG "C5'" "H5'2" sing N N 129 FAG "C4'" "O4'" sing N N 130 FAG "C4'" "C3'" sing N N 131 FAG "C4'" "H4'" sing N N 132 FAG "O4'" "C1'" sing N N 133 FAG "C1'" N9 sing N N 134 FAG "C1'" "C2'" sing N N 135 FAG "C1'" "H1'" sing N N 136 FAG N9 C4 sing N N 137 FAG N9 HN9 sing N N 138 FAG C4 N3 sing N N 139 FAG C4 C5 doub N N 140 FAG N3 C2 doub N N 141 FAG C2 N2 sing N N 142 FAG C2 N1 sing N N 143 FAG N2 HN21 sing N N 144 FAG N2 HN22 sing N N 145 FAG N1 C6 sing N N 146 FAG N1 H1 sing N N 147 FAG C6 O6 doub N N 148 FAG C6 C5 sing N N 149 FAG C5 N7 sing N N 150 FAG N7 C8 sing N N 151 FAG N7 C8A sing N N 152 FAG C8 O8 doub N N 153 FAG C8 H8 sing N N 154 FAG "C2'" "C3'" sing N N 155 FAG "C2'" "H2'1" sing N N 156 FAG "C2'" "H2'2" sing N N 157 FAG "C3'" "O3'" sing N N 158 FAG "C3'" "H3'" sing N N 159 FAG "O3'" "HO3'" sing N N 160 FAG C8A C9 sing N N 161 FAG C8A O7 sing N N 162 FAG C8A H8A sing N N 163 FAG C9 O9 sing N N 164 FAG C9 C9A sing N N 165 FAG C9 H9 sing N N 166 FAG O9 HO9 sing N N 167 FAG C9A C9B sing N N 168 FAG C9A C6A sing N N 169 FAG C9A H9A sing N N 170 FAG C9B C5M doub Y N 171 FAG C9B CAA sing Y N 172 FAG O7 C6A sing N N 173 FAG C6A O6A sing N N 174 FAG C6A H6A sing N N 175 FAG O6A C5M sing N N 176 FAG C5M C5B sing Y N 177 FAG C5B C4B doub Y N 178 FAG C5B H5B sing N N 179 FAG C4B O4 sing N N 180 FAG C4B C4A sing Y N 181 FAG O4 CM sing N N 182 FAG CM HM1 sing N N 183 FAG CM HM2 sing N N 184 FAG CM HM3 sing N N 185 FAG C4A CAA doub Y N 186 FAG CAA O10 sing N N 187 FAG O10 C11 sing N N 188 FAG C11 O11 doub N N 189 FAG C11 CBA sing N N 190 FAG P O3P sing N N 191 FAG O3P HOP3 sing N N 192 # _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model Advance _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Advance' # _atom_sites.entry_id 2KH4 _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_