data_2HMD # _entry.id 2HMD # _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 2HMD pdb_00002hmd 10.2210/pdb2hmd/pdb RCSB RCSB038512 ? ? WWPDB D_1000038512 ? ? # 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 5 'Structure model' 1 4 2024-05-29 # _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 4 'Structure model' struct_conn 7 5 'Structure model' chem_comp_atom 8 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' 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' # _pdbx_database_status.entry_id 2HMD _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_ _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 2HMR 'S-methyl stereochemistry' unspecified # 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_ _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_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 # _exptl.entry_id 2HMD _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2HMD _struct.title ;Stereochemistry Modulates Stability of Reduced Inter-Strand Cross-Links Arising From R- and S-alpha-methyl-gamma-OH-1,N2-propano-2'-Deoxyguanine 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 2HMD _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 ? # 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 2HMD 2HMD ? ? ? 2 2 PDB 2HMD 2HMD ? ? ? # 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 2HMD A 1 ? 12 ? 2HMD 1 ? 12 ? 1 12 2 2 2HMD B 1 ? 12 ? 2HMD 13 ? 24 ? 13 24 # _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 # _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 ? ? ? ? ? ? ? 1.602 ? ? 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 ? ? ? ? ? ? ? 1.541 ? ? covale4 covale both ? B DC 6 "O3'" ? ? ? 1_555 B 2EG 7 P ? ? B DC 18 B 2EG 19 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale5 covale one ? B 2EG 7 "O3'" ? ? ? 1_555 B DC 8 P ? ? B 2EG 19 B DC 20 1_555 ? ? ? ? ? ? ? 1.590 ? ? 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 ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 113.08 108.30 4.78 0.30 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.29 108.30 2.99 0.30 N 3 1 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 116.72 121.90 -5.18 0.70 N 4 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 112.01 108.30 3.71 0.30 N 5 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.20 122.90 -3.70 0.60 N 6 1 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.44 117.00 -3.56 0.50 N 7 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 121.71 117.70 4.01 0.50 N 8 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 113.68 118.60 -4.92 0.60 N 9 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.37 108.30 2.07 0.30 N 10 1 "C5'" A DC 6 ? ? "C4'" A DC 6 ? ? "O4'" A DC 6 ? ? 116.64 109.80 6.84 1.10 N 11 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 110.80 108.30 2.50 0.30 N 12 1 C4 A DA 8 ? ? C5 A DA 8 ? ? C6 A DA 8 ? ? 113.26 117.00 -3.74 0.50 N 13 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 121.86 117.70 4.16 0.50 N 14 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 112.84 118.60 -5.76 0.60 N 15 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 111.19 108.30 2.89 0.30 N 16 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 115.93 119.90 -3.97 0.60 N 17 1 C6 A DT 10 ? ? C5 A DT 10 ? ? C7 A DT 10 ? ? 119.28 122.90 -3.62 0.60 N 18 1 N3 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 117.16 121.90 -4.74 0.70 N 19 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 110.40 108.30 2.10 0.30 N 20 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 110.14 108.30 1.84 0.30 N 21 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 113.19 108.30 4.89 0.30 N 22 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 121.70 117.70 4.00 0.50 N 23 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 113.42 118.60 -5.18 0.60 N 24 1 "C3'" B DA 15 ? ? "O3'" B DA 15 ? ? P B DC 16 ? ? 127.38 119.70 7.68 1.20 Y 25 1 N1 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 122.55 118.90 3.65 0.60 N 26 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 117.43 121.90 -4.47 0.70 N 27 1 C6 B DT 17 ? ? C5 B DT 17 ? ? C7 B DT 17 ? ? 118.98 122.90 -3.92 0.60 N 28 1 N3 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 117.26 121.90 -4.64 0.70 N 29 1 N1 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 122.71 118.90 3.81 0.60 N 30 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 116.87 121.90 -5.03 0.70 N 31 1 "O4'" B DA 22 ? ? "C1'" B DA 22 ? ? N9 B DA 22 ? ? 110.29 108.30 1.99 0.30 N 32 1 C4 B DA 22 ? ? C5 B DA 22 ? ? C6 B DA 22 ? ? 113.39 117.00 -3.61 0.50 N 33 1 C5 B DA 22 ? ? C6 B DA 22 ? ? N1 B DA 22 ? ? 121.52 117.70 3.82 0.50 N 34 1 N1 B DA 22 ? ? C6 B DA 22 ? ? N6 B DA 22 ? ? 113.84 118.60 -4.76 0.60 N 35 1 "O4'" B DG 23 ? ? "C1'" B DG 23 ? ? N9 B DG 23 ? ? 111.41 108.30 3.11 0.30 N 36 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 111.23 108.30 2.93 0.30 N 37 1 N3 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 117.67 121.90 -4.23 0.70 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DT A 3 ? ? 0.060 'SIDE CHAIN' 2 1 DC A 6 ? ? 0.108 'SIDE CHAIN' 3 1 DC B 18 ? ? 0.061 'SIDE CHAIN' # 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_nmr_ensemble.entry_id 2HMD _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 2HMD _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 ;2 mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA ; '99.996% D2O' 2 ;2 mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA ; '9:1 H2O:D2O' # 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_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 # _pdbx_nmr_details.entry_id 2HMD _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_refine.entry_id 2HMD _pdbx_nmr_refine.method 'distance geometry; simulated annealing; molecular dynamics; matrix relaxation' _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 collection 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 # 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 2EG OP3 O N N 1 2EG OP1 O N N 2 2EG P P N N 3 2EG OP2 O N N 4 2EG "O5'" O N N 5 2EG "C5'" C N N 6 2EG "C4'" C N R 7 2EG "O4'" O N N 8 2EG "C3'" C N S 9 2EG "O3'" O N N 10 2EG "C2'" C N N 11 2EG "C1'" C N R 12 2EG N9 N Y N 13 2EG C4 C Y N 14 2EG N3 N N N 15 2EG C8 C Y N 16 2EG N7 N Y N 17 2EG C5 C Y N 18 2EG C6 C N N 19 2EG O6 O N N 20 2EG N1 N N N 21 2EG C2 C N N 22 2EG N2 N N N 23 2EG C21 C N N 24 2EG C22 C N N 25 2EG "H5'" H N N 26 2EG "H5''" H N N 27 2EG "H4'" H N N 28 2EG "H3'" H N N 29 2EG "H2'" H N N 30 2EG "H2''" H N N 31 2EG "H1'" H N N 32 2EG H8 H N N 33 2EG H1 H N N 34 2EG H21 H N N 35 2EG H211 H N N 36 2EG H212 H N N 37 2EG H221 H N N 38 2EG H222 H N N 39 2EG H223 H N N 40 2EG HO1 H N N 41 2EG HO2 H N N 42 2EG HO3 H N N 43 DA OP3 O N N 44 DA P P N N 45 DA OP1 O N N 46 DA OP2 O N N 47 DA "O5'" O N N 48 DA "C5'" C N N 49 DA "C4'" C N R 50 DA "O4'" O N N 51 DA "C3'" C N S 52 DA "O3'" O N N 53 DA "C2'" C N N 54 DA "C1'" C N R 55 DA N9 N Y N 56 DA C8 C Y N 57 DA N7 N Y N 58 DA C5 C Y N 59 DA C6 C Y N 60 DA N6 N N N 61 DA N1 N Y N 62 DA C2 C Y N 63 DA N3 N Y N 64 DA C4 C Y N 65 DA HOP3 H N N 66 DA HOP2 H N N 67 DA "H5'" H N N 68 DA "H5''" H N N 69 DA "H4'" H N N 70 DA "H3'" H N N 71 DA "HO3'" H N N 72 DA "H2'" H N N 73 DA "H2''" H N N 74 DA "H1'" H N N 75 DA H8 H N N 76 DA H61 H N N 77 DA H62 H N N 78 DA H2 H N N 79 DC OP3 O N N 80 DC P P N N 81 DC OP1 O N N 82 DC OP2 O N N 83 DC "O5'" O N N 84 DC "C5'" C N N 85 DC "C4'" C N R 86 DC "O4'" O N N 87 DC "C3'" C N S 88 DC "O3'" O N N 89 DC "C2'" C N N 90 DC "C1'" C N R 91 DC N1 N N N 92 DC C2 C N N 93 DC O2 O N N 94 DC N3 N N N 95 DC C4 C N N 96 DC N4 N N N 97 DC C5 C N N 98 DC C6 C N N 99 DC HOP3 H N N 100 DC HOP2 H N N 101 DC "H5'" H N N 102 DC "H5''" H N N 103 DC "H4'" H N N 104 DC "H3'" H N N 105 DC "HO3'" H N N 106 DC "H2'" H N N 107 DC "H2''" H N N 108 DC "H1'" H N N 109 DC H41 H N N 110 DC H42 H N N 111 DC H5 H N N 112 DC H6 H N N 113 DG OP3 O N N 114 DG P P N N 115 DG OP1 O N N 116 DG OP2 O N N 117 DG "O5'" O N N 118 DG "C5'" C N N 119 DG "C4'" C N R 120 DG "O4'" O N N 121 DG "C3'" C N S 122 DG "O3'" O N N 123 DG "C2'" C N N 124 DG "C1'" C N R 125 DG N9 N Y N 126 DG C8 C Y N 127 DG N7 N Y N 128 DG C5 C Y N 129 DG C6 C N N 130 DG O6 O N N 131 DG N1 N N N 132 DG C2 C N N 133 DG N2 N N N 134 DG N3 N N N 135 DG C4 C Y N 136 DG HOP3 H N N 137 DG HOP2 H N N 138 DG "H5'" H N N 139 DG "H5''" H N N 140 DG "H4'" H N N 141 DG "H3'" H N N 142 DG "HO3'" H N N 143 DG "H2'" H N N 144 DG "H2''" H N N 145 DG "H1'" H N N 146 DG H8 H N N 147 DG H1 H N N 148 DG H21 H N N 149 DG H22 H N N 150 DT OP3 O N N 151 DT P P N N 152 DT OP1 O N N 153 DT OP2 O N N 154 DT "O5'" O N N 155 DT "C5'" C N N 156 DT "C4'" C N R 157 DT "O4'" O N N 158 DT "C3'" C N S 159 DT "O3'" O N N 160 DT "C2'" C N N 161 DT "C1'" C N R 162 DT N1 N N N 163 DT C2 C N N 164 DT O2 O N N 165 DT N3 N N N 166 DT C4 C N N 167 DT O4 O N N 168 DT C5 C N N 169 DT C7 C N N 170 DT C6 C N N 171 DT HOP3 H N N 172 DT HOP2 H N N 173 DT "H5'" H N N 174 DT "H5''" H N N 175 DT "H4'" H N N 176 DT "H3'" H N N 177 DT "HO3'" H N N 178 DT "H2'" H N N 179 DT "H2''" H N N 180 DT "H1'" H N N 181 DT H3 H N N 182 DT H71 H N N 183 DT H72 H N N 184 DT H73 H N N 185 DT H6 H N N 186 # 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 2EG OP3 P doub N N 1 2EG OP1 P sing N N 2 2EG P OP2 sing N N 3 2EG P "O5'" sing N N 4 2EG "O5'" "C5'" sing N N 5 2EG "C5'" "C4'" sing N N 6 2EG "C5'" "H5'" sing N N 7 2EG "C5'" "H5''" sing N N 8 2EG "C4'" "O4'" sing N N 9 2EG "C4'" "C3'" sing N N 10 2EG "C4'" "H4'" sing N N 11 2EG "O4'" "C1'" sing N N 12 2EG "C3'" "O3'" sing N N 13 2EG "C3'" "C2'" sing N N 14 2EG "C3'" "H3'" sing N N 15 2EG "C2'" "C1'" sing N N 16 2EG "C2'" "H2'" sing N N 17 2EG "C2'" "H2''" sing N N 18 2EG "C1'" N9 sing N N 19 2EG "C1'" "H1'" sing N N 20 2EG N9 C4 sing Y N 21 2EG N9 C8 sing Y N 22 2EG C4 N3 sing N N 23 2EG C4 C5 doub Y N 24 2EG N3 C2 doub N N 25 2EG C8 N7 doub Y N 26 2EG C8 H8 sing N N 27 2EG N7 C5 sing Y N 28 2EG C5 C6 sing N N 29 2EG C6 O6 doub N N 30 2EG C6 N1 sing N N 31 2EG N1 C2 sing N N 32 2EG N1 H1 sing N N 33 2EG C2 N2 sing N N 34 2EG N2 C21 sing N N 35 2EG N2 H21 sing N N 36 2EG C21 C22 sing N N 37 2EG C21 H211 sing N N 38 2EG C21 H212 sing N N 39 2EG C22 H221 sing N N 40 2EG C22 H222 sing N N 41 2EG C22 H223 sing N N 42 2EG HO1 "O3'" sing N N 43 2EG HO2 OP2 sing N N 44 2EG HO3 OP1 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2HMD 'double helix' 2HMD '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 -0.550 -0.181 0.100 6.494 4.397 -0.485 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DC 2 1_555 B DG 11 1_555 0.359 -0.114 0.341 -3.351 -5.239 -2.004 2 A_DC2:DG23_B A 2 ? B 23 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 0.041 -0.045 0.051 1.562 -7.699 -1.907 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 -0.116 -0.065 0.040 -7.634 -12.766 -2.310 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DG 5 1_555 B DC 8 1_555 -0.115 -0.108 0.152 -2.073 -11.925 -3.984 5 A_DG5:DC20_B A 5 ? B 20 ? 19 1 1 A DC 6 1_555 B 2EG 7 1_555 0.248 -0.056 0.106 -6.716 -7.907 -6.500 6 A_DC6:2EG19_B A 6 ? B 19 ? 19 1 1 A 2EG 7 1_555 B DC 6 1_555 -0.537 -0.144 0.021 4.607 -8.300 -1.839 7 A_2EG7:DC18_B A 7 ? B 18 ? 19 1 1 A DA 8 1_555 B DT 5 1_555 0.435 0.040 0.028 0.352 -12.610 -2.382 8 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.340 -0.148 0.302 1.140 -10.431 -2.236 9 A_DG9:DC16_B A 9 ? B 16 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.111 0.109 0.118 -9.076 -11.174 -5.000 10 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.465 -0.143 -0.146 -6.870 1.754 -1.138 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DC 12 1_555 B DG 1 1_555 0.784 -0.177 0.246 -10.149 5.777 2.266 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 -0.724 -0.999 3.596 -2.673 -0.284 37.525 -1.509 0.738 3.644 -0.441 4.148 37.617 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 0.105 -1.225 3.089 3.157 1.131 30.409 -2.532 0.388 3.038 2.148 -5.995 30.589 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 -1.002 -0.338 3.422 -2.259 4.362 35.533 -1.205 1.288 3.414 7.106 3.680 35.860 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 0.048 -0.999 3.177 -0.511 0.779 29.160 -2.148 -0.202 3.148 1.547 1.014 29.175 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 0.424 -0.573 3.370 1.633 2.249 41.256 -1.060 -0.421 3.349 3.187 -2.314 41.345 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 0.003 0.181 3.051 2.036 6.373 20.278 -1.968 0.775 2.954 17.497 -5.591 21.342 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 -0.415 -0.047 3.373 -1.990 6.042 43.340 -0.658 0.361 3.352 8.129 2.678 43.782 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 0.138 -0.700 3.155 -3.228 1.302 28.034 -1.725 -1.001 3.085 2.675 6.631 28.245 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 -0.233 -1.023 3.526 2.828 2.125 34.523 -2.062 0.852 3.429 3.569 -4.749 34.698 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 1.222 0.129 3.222 4.428 2.722 41.403 -0.106 -1.248 3.331 3.831 -6.233 41.714 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 -0.213 -1.169 3.509 -3.710 -2.908 37.093 -1.407 -0.200 3.591 -4.549 5.804 37.381 11 AA_DC11DC12:DG13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # 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 ? # _atom_sites.entry_id 2HMD _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_