data_2AWV # _entry.id 2AWV # _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 2AWV pdb_00002awv 10.2210/pdb2awv/pdb RCSB RCSB034409 ? ? WWPDB D_1000034409 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-09-20 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_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' struct_conn 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2AWV _pdbx_database_status.recvd_initial_deposition_date 2005-09-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Q2T 'i-motif structurewithcomparable organisation' unspecified PDB 1RME 'i-motif structurewithcomparable organisation' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Canalia, M.' 1 'Leroy, J.-L.' 2 # _citation.id primary _citation.title 'Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC).' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 5471 _citation.page_last 5481 _citation.year 2005 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16204453 _citation.pdbx_database_id_DOI 10.1093/nar/gki843 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Canalia, M.' 1 ? primary 'Leroy, J.-L.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3'" _entity.formula_weight 2545.773 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MCY)(DC)(DT)(DC)(DA)(DC)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can CCTCACTCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MCY n 1 2 DC n 1 3 DT n 1 4 DC n 1 5 DA n 1 6 DC n 1 7 DT n 1 8 DC n 1 9 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'chemicaly synthetized using the phosphoramidite method' # 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 MCY 'DNA linking' n "5-METHYL-2'-DEOXYCYTIDINE" ? 'C10 H15 N3 O4' 241.244 # 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 MCY 1 1 1 MCY CYT 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 DC 4 4 4 DC C A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DC 9 9 9 DC C A . n B 1 1 MCY 1 1 1 MCY CYT B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DC 4 4 4 DC C B . n B 1 5 DA 5 5 5 DA A B . n B 1 6 DC 6 6 6 DC C B . n B 1 7 DT 7 7 7 DT T B . n B 1 8 DC 8 8 8 DC C B . n B 1 9 DC 9 9 9 DC C B . n # _exptl.entry_id 2AWV _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 2AWV _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2AWV _struct.title 'NMR Structural Analysis of the dimer of 5MCCTCATCC' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2AWV _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'i-motif, hemiprotonated CC+ pairs, dimer, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2AWV _struct_ref.pdbx_db_accession 2AWV _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2AWV A 1 ? 9 ? 2AWV 1 ? 9 ? 1 9 2 1 2AWV B 1 ? 9 ? 2AWV 1 ? 9 ? 1 9 # _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 MCY 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A MCY 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale2 covale both ? B MCY 1 "O3'" ? ? ? 1_555 B DC 2 P ? ? B MCY 1 B DC 2 1_555 ? ? ? ? ? ? ? 1.615 ? ? hydrog1 hydrog ? ? A MCY 1 N3 ? ? ? 1_555 B MCY 1 N4 ? ? A MCY 1 B MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog2 hydrog ? ? A MCY 1 N4 ? ? ? 1_555 B MCY 1 N3 ? ? A MCY 1 B MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DC 2 N4 ? ? A DC 2 B DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DC 2 N3 ? ? A DC 2 B DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DT 7 O4 ? ? A DC 2 B DT 7 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog6 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DC 4 O2 ? ? A DC 4 B DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DC 4 N4 ? ? A DC 4 B DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DC 6 O2 ? ? A DC 6 B DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DC 6 N4 ? ? A DC 6 B DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DC 2 N4 ? ? A DT 7 B DC 2 1_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DT 7 O4 ? ? A DT 7 B DT 7 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DT 7 N3 ? ? A DT 7 B DT 7 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog13 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DC 8 O2 ? ? A DC 8 B DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog14 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DC 8 N4 ? ? A DC 8 B DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog15 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DC 9 O2 ? ? A DC 9 B DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog16 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DC 9 N4 ? ? A DC 9 B DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H41 A DC 2 ? ? N3 B DC 2 ? ? 1.43 2 1 O4 A DT 7 ? ? H3 B DT 7 ? ? 1.54 3 1 N3 A DC 2 ? ? H41 B DC 2 ? ? 1.54 4 1 H3 A DT 7 ? ? O4 B DT 7 ? ? 1.58 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.91 108.30 2.61 0.30 N 2 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 112.33 108.30 4.03 0.30 N 3 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 111.41 108.30 3.11 0.30 N 4 1 N7 A DA 5 ? ? C8 A DA 5 ? ? N9 A DA 5 ? ? 117.37 113.80 3.57 0.50 N 5 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 112.79 108.30 4.49 0.30 N 6 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 112.97 108.30 4.67 0.30 N 7 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 112.00 108.30 3.70 0.30 N 8 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 110.29 108.30 1.99 0.30 N 9 1 "O4'" B DT 3 ? ? "C1'" B DT 3 ? ? N1 B DT 3 ? ? 110.90 108.30 2.60 0.30 N 10 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 112.35 108.30 4.05 0.30 N 11 1 "O4'" B DA 5 ? ? "C1'" B DA 5 ? ? N9 B DA 5 ? ? 111.42 108.30 3.12 0.30 N 12 1 N7 B DA 5 ? ? C8 B DA 5 ? ? N9 B DA 5 ? ? 117.44 113.80 3.64 0.50 N 13 1 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 112.94 108.30 4.64 0.30 N 14 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 113.02 108.30 4.72 0.30 N 15 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 111.98 108.30 3.68 0.30 N 16 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 110.24 108.30 1.94 0.30 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 MCY 1 A MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 2 B MCY 1 B MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" # _pdbx_nmr_ensemble.entry_id 2AWV _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 2AWV _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'strand concentration: 0.1 to 10mM' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength '1 Na / phosphate' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 E-COSY 1 3 1 '1H-31P COSY' 1 # _pdbx_nmr_details.entry_id 2AWV _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear and heteronuclear techniques' # _pdbx_nmr_refine.entry_id 2AWV _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;the structure is based on 565 NOE-derived, distance constraints, 17 dihedral angle restraints, 20 distance restraints from hydrogen bonds. ; _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 processing Felix 97.2 'Hare D.' 1 'structure solution' X-PLOR 3.851 'Brunger A' 2 'data analysis' MOLMOL 2.4 'Koradi,R.,Billeter, M and W trich, K.' 3 refinement X-PLOR 3.851 ? 4 # 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 MCY N1 N N N 107 MCY C2 C N N 108 MCY N3 N N N 109 MCY C4 C N N 110 MCY C5 C N N 111 MCY C6 C N N 112 MCY O2 O N N 113 MCY N4 N N N 114 MCY "C1'" C N R 115 MCY "C2'" C N N 116 MCY "C3'" C N S 117 MCY "C4'" C N R 118 MCY "O4'" O N N 119 MCY "O3'" O N N 120 MCY "C5'" C N N 121 MCY "O5'" O N N 122 MCY C5A C N N 123 MCY H6 H N N 124 MCY HN41 H N N 125 MCY HN42 H N N 126 MCY "H1'" H N N 127 MCY "H2'" H N N 128 MCY "H2''" H N N 129 MCY "H3'" H N N 130 MCY "H4'" H N N 131 MCY "HO3'" H N N 132 MCY "H5'" H N N 133 MCY "H5''" H N N 134 MCY "HO5'" H N N 135 MCY H5A1 H N N 136 MCY H5A2 H N N 137 MCY H5A3 H N N 138 # 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 MCY N1 C2 sing N N 111 MCY N1 C6 sing N N 112 MCY N1 "C1'" sing N N 113 MCY C2 N3 sing N N 114 MCY C2 O2 doub N N 115 MCY N3 C4 doub N N 116 MCY C4 C5 sing N N 117 MCY C4 N4 sing N N 118 MCY C5 C6 doub N N 119 MCY C5 C5A sing N N 120 MCY C6 H6 sing N N 121 MCY N4 HN41 sing N N 122 MCY N4 HN42 sing N N 123 MCY "C1'" "C2'" sing N N 124 MCY "C1'" "O4'" sing N N 125 MCY "C1'" "H1'" sing N N 126 MCY "C2'" "C3'" sing N N 127 MCY "C2'" "H2'" sing N N 128 MCY "C2'" "H2''" sing N N 129 MCY "C3'" "C4'" sing N N 130 MCY "C3'" "O3'" sing N N 131 MCY "C3'" "H3'" sing N N 132 MCY "C4'" "O4'" sing N N 133 MCY "C4'" "C5'" sing N N 134 MCY "C4'" "H4'" sing N N 135 MCY "O3'" "HO3'" sing N N 136 MCY "C5'" "O5'" sing N N 137 MCY "C5'" "H5'" sing N N 138 MCY "C5'" "H5''" sing N N 139 MCY "O5'" "HO5'" sing N N 140 MCY C5A H5A1 sing N N 141 MCY C5A H5A2 sing N N 142 MCY C5A H5A3 sing N N 143 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2AWV 'double helix' 2AWV 'parallel strands' 2AWV 'mismatched base pair' 2AWV 'internal loop' # 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 DC 4 1_555 B DC 4 1_555 2.470 2.198 0.004 15.171 1.316 179.986 1 A_DC4:DC4_B A 4 ? B 4 ? 15 2 1 A DC 6 1_555 B DC 6 1_555 -2.328 -2.127 -0.011 4.883 13.315 -179.985 2 A_DC6:DC6_B A 6 ? B 6 ? 15 2 1 A DT 7 1_555 B DT 7 1_555 2.178 -2.294 0.053 -5.963 7.585 179.866 3 A_DT7:DT7_B A 7 ? B 7 ? 12 2 1 A DC 2 1_555 B DC 2 1_555 2.226 -0.442 -0.085 -6.668 -30.320 179.527 4 A_DC2:DC2_B A 2 ? B 2 ? 14 2 1 A DC 8 1_555 B DC 8 1_555 2.329 2.076 -0.029 -14.472 -1.014 179.892 5 A_DC8:DC8_B A 8 ? B 8 ? 15 2 1 A MCY 1 1_555 B MCY 1 1_555 -2.120 -0.105 -0.004 -5.567 -15.619 -179.892 6 A_MCY1:MCY1_B A 1 ? B 1 ? 14 2 1 A DC 9 1_555 B DC 9 1_555 2.488 2.111 -0.006 -15.077 5.434 179.968 7 A_DC9:DC9_B A 9 ? B 9 ? 15 2 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 4 1_555 B DC 4 1_555 A DC 6 1_555 B DC 6 1_555 2.579 1.974 -0.001 -109.286 142.853 122.726 0.987 -1.289 -0.001 71.433 54.648 179.934 1 AA_DC4DC6:DC6DC4_BB A 4 ? B 4 ? A 6 ? B 6 ? 1 A DC 6 1_555 B DC 6 1_555 A DT 7 1_555 B DT 7 1_555 0.006 0.008 3.174 0.396 -0.075 174.738 0.004 -0.003 3.174 -0.037 -0.198 174.738 2 AA_DC6DT7:DT7DC6_BB A 6 ? B 6 ? A 7 ? B 7 ? 1 A DT 7 1_555 B DT 7 1_555 A DC 2 1_555 B DC 2 1_555 1.948 -1.087 0.041 -85.960 -156.976 -0.193 0.554 0.969 -0.018 78.939 -43.227 -178.971 3 AA_DT7DC2:DC2DT7_BB A 7 ? B 7 ? A 2 ? B 2 ? 1 A DC 2 1_555 B DC 2 1_555 A DC 8 1_555 B DC 8 1_555 2.646 -3.119 0.011 136.866 115.872 83.923 -1.563 -1.319 0.011 58.008 -68.518 179.500 4 AA_DC2DC8:DC8DC2_BB A 2 ? B 2 ? A 8 ? B 8 ? 1 A DC 8 1_555 B DC 8 1_555 A MCY 1 1_555 B MCY 1 1_555 -2.316 -2.588 0.003 -133.907 119.774 -112.130 1.293 -1.158 0.002 -59.906 -66.975 -179.809 5 AA_DC8MCY1:MCY1DC8_BB A 8 ? B 8 ? A 1 ? B 1 ? 1 A MCY 1 1_555 B MCY 1 1_555 A DC 9 1_555 B DC 9 1_555 -1.937 -1.332 -0.002 102.057 -148.037 98.008 -0.667 0.968 -0.003 -74.038 -51.042 179.873 6 AA_MCY1DC9:DC9MCY1_BB A 1 ? B 1 ? A 9 ? B 9 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.type ? # _atom_sites.entry_id 2AWV _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_