data_2HMR # _entry.id 2HMR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2HMR pdb_00002hmr 10.2210/pdb2hmr/pdb RCSB RCSB038523 ? ? WWPDB D_1000038523 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2HLI 'S-methyl stereochemistry but opened species (cross-link precursor)' unspecified PDB 2HMD 'R-methyl stereochemistry' unspecified # _pdbx_database_status.entry_id 2HMR _pdbx_database_status.status_code REL _pdbx_database_status.recvd_initial_deposition_date 2006-07-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cho, Y.-J.' 1 'Kozekov, I.D.' 2 'Harris, T.M.' 3 'Rizzo, C.J.' 4 'Stone, M.P.' 5 # _citation.id primary _citation.title ;Stereochemistry Modulates the Stability of Reduced Interstrand Cross-Links Arising from R- and S-alpha-CH(3)-gamma-OH-1,N(2)-Propano-2'-deoxyguanosine in the 5'-CpG-3' DNA Sequence ; _citation.journal_abbrev Biochemistry _citation.journal_volume 46 _citation.page_first 2608 _citation.page_last 2621 _citation.year 2007 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17305317 _citation.pdbx_database_id_DOI 10.1021/bi061381h # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cho, Y.-J.' 1 ? primary 'Kozekov, I.D.' 2 ? primary 'Harris, T.M.' 3 ? primary 'Rizzo, C.J.' 4 ? primary 'Stone, M.P.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'DNA dodecamer with interstrand cross-link' 3691.445 1 ? ? ? 'G7 of chain A and B linked' 2 polymer syn 'DNA dodecamer with interstrand cross-link' 3691.445 1 ? ? ? 'G7 of chain A and B linked' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DG)(DC)(DT)(DA)(DG)(DC)(2EG)(DA)(DG)(DT)(DC)(DC)' GCTAGCGAGTCC A ? 2 polydeoxyribonucleotide no yes '(DG)(DG)(DA)(DC)(DT)(DC)(2EG)(DC)(DT)(DA)(DG)(DC)' GGACTCGCTAGC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DT n 1 4 DA n 1 5 DG n 1 6 DC n 1 7 2EG n 1 8 DA n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC n 2 1 DG n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DT n 2 6 DC n 2 7 2EG n 2 8 DC n 2 9 DT n 2 10 DA n 2 11 DG n 2 12 DC n # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2HMR 2HMR ? ? ? 2 2 PDB 2HMR 2HMR ? ? ? # 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 2HMR A 1 ? 12 ? 2HMR 1 ? 12 ? 1 12 2 2 2HMR B 1 ? 12 ? 2HMR 13 ? 24 ? 13 24 # 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 2EG 'DNA linking' n ;2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE ; ? 'C12 H18 N5 O7 P' 375.274 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 DQF-COSY 1 3 1 '2D TOCSY' 1 4 2 '2D NOESY' 2 # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 303 1 7.0 '0.1M NaCl' atm K 2 286 1 7.0 '0.1M NaCl' atm K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '2mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA' '99.996% D2O' 2 '2mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA' '9:1 H2O:D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 AVANCE Bruker 800 ? 2 AVANCE Bruker 600 ? 3 AVANCE Bruker 500 ? # _pdbx_nmr_refine.entry_id 2HMR _pdbx_nmr_refine.method ;distance geometry simulated annealing molecular dynamics matrix relaxation ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2HMR _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 2HMR _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _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 2HMR _pdbx_nmr_representative.conformer_id 10 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal processing XwinNMR 3.5 Bruker 1 processing NMRPipe 2.3 'Delaglio F et al.' 2 'data analysis' Felix 2000 'Accelrys, Inc.' 3 'iterative matrix relaxation' MARDIGRAS 5.2.1 'Borgias, B.A. et al.' 4 refinement Amber 8.0 'Case et al' 5 'data analysis' CORMA 5.2 'Keepers JW et al.' 6 # _exptl.entry_id 2HMR _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2HMR _struct.title ;Solution structure of reduced interstrand cross-link arising from S-alpha-methyl-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2HMR _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'crotonaldehyde interstrand DNA cross-link, 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 2 ? # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DC 6 "O3'" ? ? ? 1_555 A 2EG 7 P ? ? A DC 6 A 2EG 7 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale one ? A 2EG 7 "O3'" ? ? ? 1_555 A DA 8 P ? ? A 2EG 7 A DA 8 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale none ? A 2EG 7 C21 ? ? ? 1_555 B 2EG 7 C22 ? ? A 2EG 7 B 2EG 19 1_555 ? ? ? ? ? ? ? 1.556 ? ? covale4 covale both ? B DC 6 "O3'" ? ? ? 1_555 B 2EG 7 P ? ? B DC 18 B 2EG 19 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale one ? B 2EG 7 "O3'" ? ? ? 1_555 B DC 8 P ? ? B 2EG 19 B DC 20 1_555 ? ? ? ? ? ? ? 1.612 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B 2EG 7 N1 ? ? A DC 6 B 2EG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B 2EG 7 O6 ? ? A DC 6 B 2EG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B 2EG 7 N2 ? ? A DC 6 B 2EG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A 2EG 7 N1 ? ? ? 1_555 B DC 6 N3 ? ? A 2EG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A 2EG 7 N2 ? ? ? 1_555 B DC 6 O2 ? ? A 2EG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A 2EG 7 O6 ? ? ? 1_555 B DC 6 N4 ? ? A 2EG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2HMR _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 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 2EG 7 7 7 2EG 2EG A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DT 10 10 10 DT T A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DC 12 12 12 DC C A . n B 2 1 DG 1 13 13 DG G B . n B 2 2 DG 2 14 14 DG G B . n B 2 3 DA 3 15 15 DA A B . n B 2 4 DC 4 16 16 DC C B . n B 2 5 DT 5 17 17 DT T B . n B 2 6 DC 6 18 18 DC C B . n B 2 7 2EG 7 19 19 2EG 2EG B . n B 2 8 DC 8 20 20 DC C B . n B 2 9 DT 9 21 21 DT T B . n B 2 10 DA 10 22 22 DA A B . n B 2 11 DG 11 23 23 DG G B . n B 2 12 DC 12 24 24 DC C B . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 2EG 7 A 2EG 7 ? G ;2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE ; 2 B 2EG 7 B 2EG 19 ? G ;2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE ; # _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 2007-03-13 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _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_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn # 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' 5 4 'Structure model' '_struct_conn.pdbx_dist_value' 6 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' # 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 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 117.06 121.90 -4.84 0.70 N 2 1 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.36 117.00 -3.64 0.50 N 3 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 121.87 117.70 4.17 0.50 N 4 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 113.47 118.60 -5.13 0.60 N 5 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 111.54 108.30 3.24 0.30 N 6 1 C4 A DA 8 ? ? C5 A DA 8 ? ? C6 A DA 8 ? ? 113.77 117.00 -3.23 0.50 N 7 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 121.36 117.70 3.66 0.50 N 8 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 112.71 118.60 -5.89 0.60 N 9 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 112.27 108.30 3.97 0.30 N 10 1 "O4'" A DT 10 ? ? "C1'" A DT 10 ? ? N1 A DT 10 ? ? 112.79 108.30 4.49 0.30 N 11 1 N3 A DT 10 ? ? C2 A DT 10 ? ? O2 A DT 10 ? ? 118.58 122.30 -3.72 0.60 N 12 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 111.63 108.30 3.33 0.30 N 13 1 N3 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 116.83 121.90 -5.07 0.70 N 14 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 110.90 108.30 2.60 0.30 N 15 1 N1 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 116.01 119.90 -3.89 0.60 N 16 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 111.60 108.30 3.30 0.30 N 17 1 C4 B DA 15 ? ? C5 B DA 15 ? ? C6 B DA 15 ? ? 113.56 117.00 -3.44 0.50 N 18 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 121.83 117.70 4.13 0.50 N 19 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 114.52 118.60 -4.08 0.60 N 20 1 "O4'" B DC 16 ? ? "C1'" B DC 16 ? ? N1 B DC 16 ? ? 112.71 108.30 4.41 0.30 N 21 1 N1 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 122.54 118.90 3.64 0.60 N 22 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 116.82 121.90 -5.08 0.70 N 23 1 C6 B DT 17 ? ? C5 B DT 17 ? ? C7 B DT 17 ? ? 119.01 122.90 -3.89 0.60 N 24 1 N3 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 116.99 121.90 -4.91 0.70 N 25 1 N1 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 122.59 118.90 3.69 0.60 N 26 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 116.59 121.90 -5.31 0.70 N 27 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 112.17 108.30 3.87 0.30 N 28 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 119.26 122.90 -3.64 0.60 N 29 1 "O4'" B DA 22 ? ? "C1'" B DA 22 ? ? N9 B DA 22 ? ? 113.29 108.30 4.99 0.30 N 30 1 C4 B DA 22 ? ? C5 B DA 22 ? ? C6 B DA 22 ? ? 113.37 117.00 -3.63 0.50 N 31 1 C5 B DA 22 ? ? C6 B DA 22 ? ? N1 B DA 22 ? ? 121.82 117.70 4.12 0.50 N 32 1 N1 B DA 22 ? ? C6 B DA 22 ? ? N6 B DA 22 ? ? 113.84 118.60 -4.76 0.60 N 33 1 N1 B DG 23 ? ? C6 B DG 23 ? ? O6 B DG 23 ? ? 116.13 119.90 -3.77 0.60 N 34 1 "C3'" B DG 23 ? ? "O3'" B DG 23 ? ? P B DC 24 ? ? 127.92 119.70 8.22 1.20 Y # 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 DC A 6 ? ? 0.083 'SIDE CHAIN' 2 1 DG B 13 ? ? 0.067 'SIDE CHAIN' 3 1 DG B 14 ? ? 0.088 'SIDE CHAIN' 4 1 DC B 18 ? ? 0.062 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2HMR 'double helix' 2HMR 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 12 1_555 -0.459 -0.186 0.511 10.537 8.003 0.607 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DC 2 1_555 B DG 11 1_555 0.367 -0.078 0.186 2.941 -3.453 -0.695 2 A_DC2:DG23_B A 2 ? B 23 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 0.127 -0.069 -0.123 3.430 -7.838 -2.557 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 -0.145 -0.067 -0.116 -8.271 -17.787 -0.759 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DG 5 1_555 B DC 8 1_555 -0.394 -0.145 0.182 -5.488 -8.270 -1.449 5 A_DG5:DC20_B A 5 ? B 20 ? 19 1 1 A DC 6 1_555 B 2EG 7 1_555 0.839 -0.175 0.395 -10.536 0.923 1.314 6 A_DC6:2EG19_B A 6 ? B 19 ? 19 1 1 A 2EG 7 1_555 B DC 6 1_555 -0.390 -0.116 0.199 12.751 -3.372 -2.904 7 A_2EG7:DC18_B A 7 ? B 18 ? 19 1 1 A DA 8 1_555 B DT 5 1_555 0.211 0.032 -0.262 2.519 -21.888 -3.477 8 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.499 -0.128 0.396 -0.287 -13.595 -3.146 9 A_DG9:DC16_B A 9 ? B 16 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.216 -0.025 0.212 -12.244 -11.896 -5.843 10 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.320 -0.075 0.077 -10.762 -9.373 -0.543 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DC 12 1_555 B DG 1 1_555 0.716 -0.179 0.366 -13.684 1.750 1.415 12 A_DC12:DG13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B DC 12 1_555 A DC 2 1_555 B DG 11 1_555 -0.500 -1.201 3.571 2.188 4.776 32.882 -2.942 1.261 3.329 8.370 -3.834 33.288 1 AA_DG1DC2:DG23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DC 2 1_555 B DG 11 1_555 A DT 3 1_555 B DA 10 1_555 0.241 -0.496 3.261 3.828 -2.170 36.115 -0.490 0.150 3.292 -3.484 -6.146 36.373 2 AA_DC2DT3:DA22DG23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DT 3 1_555 B DA 10 1_555 A DA 4 1_555 B DT 9 1_555 0.033 -1.063 3.326 1.071 15.245 32.124 -3.867 0.095 2.576 25.805 -1.813 35.487 3 AA_DT3DA4:DT21DA22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DG 5 1_555 B DC 8 1_555 -0.453 -0.794 3.175 -3.437 0.002 30.474 -1.502 0.194 3.206 0.004 6.513 30.663 4 AA_DA4DG5:DC20DT21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B DC 8 1_555 A DC 6 1_555 B 2EG 7 1_555 0.301 -0.250 3.370 -1.815 1.448 44.073 -0.472 -0.576 3.346 1.928 2.417 44.131 5 AA_DG5DC6:2EG19DC20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DC 6 1_555 B 2EG 7 1_555 A 2EG 7 1_555 B DC 6 1_555 -0.474 0.303 2.830 3.505 1.304 22.411 0.367 2.287 2.737 3.324 -8.938 22.717 6 AA_DC62EG7:DC182EG19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A 2EG 7 1_555 B DC 6 1_555 A DA 8 1_555 B DT 5 1_555 -0.496 -0.116 3.607 0.820 8.248 37.077 -1.335 0.877 3.491 12.775 -1.270 37.960 7 AA_2EG7DA8:DT17DC18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DA 8 1_555 B DT 5 1_555 A DG 9 1_555 B DC 4 1_555 0.254 -0.458 3.268 -6.878 3.614 32.517 -1.385 -1.563 3.084 6.342 12.070 33.409 8 AA_DA8DG9:DC16DT17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DG 9 1_555 B DC 4 1_555 A DT 10 1_555 B DA 3 1_555 -0.236 -0.998 3.645 2.726 0.542 35.256 -1.732 0.835 3.602 0.893 -4.493 35.361 9 AA_DG9DT10:DA15DC16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DT 10 1_555 B DA 3 1_555 A DC 11 1_555 B DG 2 1_555 0.589 0.059 3.179 2.349 2.937 38.583 -0.262 -0.607 3.203 4.433 -3.544 38.759 10 AA_DT10DC11:DG14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DC 12 1_555 B DG 1 1_555 0.460 -1.110 3.362 -1.167 2.387 33.597 -2.309 -0.986 3.260 4.121 2.015 33.699 11 AA_DC11DC12:DG13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? #