data_8Y1I # _entry.id 8Y1I # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.399 _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 8Y1I pdb_00008y1i 10.2210/pdb8y1i/pdb WWPDB D_1300044628 ? ? BMRB 36641 ? 10.13018/BMR36641 # 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 2024-12-04 2 'Structure model' 1 1 2024-12-11 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # 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 2 'Structure model' '_citation.pdbx_database_id_PubMed' 2 2 'Structure model' '_citation.title' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 8Y1I _pdbx_database_status.recvd_initial_deposition_date 2024-01-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs . _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name BMRB _pdbx_database_related.details ;Structure of guanosine-2''-fluorinated [d(AACCGGTT)]2 ; _pdbx_database_related.db_id 36641 _pdbx_database_related.content_type unspecified # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 gltang@sioc.ac.cn Tang Gong-Li ? 'principal investigator/group leader' 0000-0003-3149-4683 3 ccao@mail.sioc.ac.cn Cao Chunyang ? 'principal investigator/group leader' 0000-0001-7865-8249 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Gao, R.Q.' 1 0009-0007-8186-5063 'Cao, C.' 2 0000-0001-7865-8249 'Tang, G.L.' 3 0000-0003-3149-4683 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Jacs Au' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2691-3704 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 4 _citation.language ? _citation.page_first 3641 _citation.page_last 3648 _citation.title 'Different DNA Binding and Damage Mode between Anticancer Antibiotics Trioxacarcin A and LL-D49194 alpha 1.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacsau.4c00611 _citation.pdbx_database_id_PubMed 39328742 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gao, R.Q.' 1 ? primary 'Hu, X.D.' 2 ? primary 'Zhou, Q.' 3 ? primary 'Hou, X.F.' 4 ? primary 'Cao, C.' 5 ? primary 'Tang, G.L.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*(3D1)P*AP*CP*CP*(GF2)P*(GF2)P*TP*T)-3') ; _entity.formula_weight 2382.619 _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 '(3D1)(DA)(DC)(DC)(GF2)(GF2)(DT)(DT)' _entity_poly.pdbx_seq_one_letter_code_can XACCXXTT _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 3D1 n 1 2 DA n 1 3 DC n 1 4 DC n 1 5 GF2 n 1 6 GF2 n 1 7 DT n 1 8 DT 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'DNA molecule' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 2853804 _pdbx_entity_src_syn.details ? # 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 3D1 non-polymer . '(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol' "2'-DEOXYADENOSINE" 'C10 H13 N5 O3' 251.242 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 GF2 'DNA linking' n ;2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O7 P' 365.212 # 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 3D1 1 1 1 3D1 ADE A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 GF2 5 5 5 GF2 FGU A . n A 1 6 GF2 6 6 6 GF2 FGU A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n B 1 1 3D1 1 9 9 3D1 ADE B . n B 1 2 DA 2 10 10 DA DA B . n B 1 3 DC 3 11 11 DC DC B . n B 1 4 DC 4 12 12 DC DC B . n B 1 5 GF2 5 13 13 GF2 FGU B . n B 1 6 GF2 6 14 14 GF2 FGU B . n B 1 7 DT 7 15 15 DT DT B . n B 1 8 DT 8 16 16 DT DT B . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id GF2 _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id GF2 _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8Y1I _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 8Y1I _struct.title ;Structure of guanosine-2''-fluorinated [d(AACCGGTT)]2 ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8Y1I _struct_keywords.text 'dimer, fluorogenic, DNA' _struct_keywords.pdbx_keywords 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.db_name PDB _struct_ref.db_code 8Y1I _struct_ref.pdbx_db_accession 8Y1I _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 8Y1I A 1 ? 8 ? 8Y1I 1 ? 8 ? 1 8 2 1 8Y1I B 1 ? 8 ? 8Y1I 9 ? 16 ? 9 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_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_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'NMR Distance Restraints' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # 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 one ? A 3D1 1 "O3'" ? ? ? 1_555 A DA 2 P ? ? A 3D1 1 A DA 2 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A DC 4 "O3'" ? ? ? 1_555 A GF2 5 P ? ? A DC 4 A GF2 5 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale3 covale one ? A GF2 5 "O3'" ? ? ? 1_555 A GF2 6 P ? ? A GF2 5 A GF2 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale one ? A GF2 6 "O3'" ? ? ? 1_555 A DT 7 P ? ? A GF2 6 A DT 7 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale5 covale one ? B 3D1 1 "O3'" ? ? ? 1_555 B DA 2 P ? ? B 3D1 9 B DA 10 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale6 covale both ? B DC 4 "O3'" ? ? ? 1_555 B GF2 5 P ? ? B DC 12 B GF2 13 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale7 covale one ? B GF2 5 "O3'" ? ? ? 1_555 B GF2 6 P ? ? B GF2 13 B GF2 14 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale8 covale one ? B GF2 6 "O3'" ? ? ? 1_555 B DT 7 P ? ? B GF2 14 B DT 15 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 2 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 2 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B GF2 6 N1 ? ? A DC 3 B GF2 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B GF2 6 O6 ? ? A DC 3 B GF2 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B GF2 6 N2 ? ? A DC 3 B GF2 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B GF2 5 N1 ? ? A DC 4 B GF2 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B GF2 5 O6 ? ? A DC 4 B GF2 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B GF2 5 N2 ? ? A DC 4 B GF2 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A GF2 5 N1 ? ? ? 1_555 B DC 4 N3 ? ? A GF2 5 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A GF2 5 N2 ? ? ? 1_555 B DC 4 O2 ? ? A GF2 5 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A GF2 5 O6 ? ? ? 1_555 B DC 4 N4 ? ? A GF2 5 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A GF2 6 N1 ? ? ? 1_555 B DC 3 N3 ? ? A GF2 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A GF2 6 N2 ? ? ? 1_555 B DC 3 O2 ? ? A GF2 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A GF2 6 O6 ? ? ? 1_555 B DC 3 N4 ? ? A GF2 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 7 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 7 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_entry_details.entry_id 8Y1I _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_protein_modification N # _pdbx_nmr_ensemble.entry_id 8Y1I _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _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 8Y1I _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ;2 mM DNA (5'-D(*(ADE)P*AP*CP*CP*(FGU)P*(FGU)P*TP*T)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O ; _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label DNA _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 ;DNA (5'-D(*(ADE)P*AP*CP*CP*(FGU)P*(FGU)P*TP*T)-3') ; 2 ? mM 'natural abundance' 1 'sodium phosphate' 10 ? mM 'natural abundance' 1 'sodium chloride' 20 ? mM 'natural abundance' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.ionic_strength 44.4 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label DNA _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H NOESY' 1 anisotropic 2 1 1 '2D 1H-1H COSY' 1 anisotropic 3 1 1 '2D 1H-1H TOCSY' 1 anisotropic # _pdbx_nmr_refine.entry_id 8Y1I _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 5 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' NMRFAM-SPARKY ? 'Woonghee Lee,* Marco Tonelli, and John L. Markley*' 2 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 collection NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 4 'peak picking' NMRFAM-SPARKY ? 'Woonghee Lee,* Marco Tonelli, and John L. Markley*' 5 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' # 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 3D1 "O5'" O N N 1 3D1 "C5'" C N N 2 3D1 "C4'" C N R 3 3D1 "O4'" O N N 4 3D1 "C1'" C N R 5 3D1 N9 N Y N 6 3D1 C4 C Y N 7 3D1 N3 N Y N 8 3D1 C2 C Y N 9 3D1 N1 N Y N 10 3D1 C6 C Y N 11 3D1 N6 N N N 12 3D1 C5 C Y N 13 3D1 N7 N Y N 14 3D1 C8 C Y N 15 3D1 "C2'" C N N 16 3D1 "C3'" C N S 17 3D1 "O3'" O N N 18 3D1 "H5'" H N N 19 3D1 "H5'1" H N N 20 3D1 "H5'2" H N N 21 3D1 "H4'" H N N 22 3D1 "H1'" H N N 23 3D1 H2 H N N 24 3D1 HN61 H N N 25 3D1 HN62 H N N 26 3D1 H8 H N N 27 3D1 "H2'1" H N N 28 3D1 "H2'2" H N N 29 3D1 "H3'" H N N 30 3D1 H1 H N N 31 DA OP3 O N N 32 DA P P N N 33 DA OP1 O N N 34 DA OP2 O N N 35 DA "O5'" O N N 36 DA "C5'" C N N 37 DA "C4'" C N R 38 DA "O4'" O N N 39 DA "C3'" C N S 40 DA "O3'" O N N 41 DA "C2'" C N N 42 DA "C1'" C N R 43 DA N9 N Y N 44 DA C8 C Y N 45 DA N7 N Y N 46 DA C5 C Y N 47 DA C6 C Y N 48 DA N6 N N N 49 DA N1 N Y N 50 DA C2 C Y N 51 DA N3 N Y N 52 DA C4 C Y N 53 DA HOP3 H N N 54 DA HOP2 H N N 55 DA "H5'" H N N 56 DA "H5''" H N N 57 DA "H4'" H N N 58 DA "H3'" H N N 59 DA "HO3'" H N N 60 DA "H2'" H N N 61 DA "H2''" H N N 62 DA "H1'" H N N 63 DA H8 H N N 64 DA H61 H N N 65 DA H62 H N N 66 DA H2 H N N 67 DC OP3 O N N 68 DC P P N N 69 DC OP1 O N N 70 DC OP2 O N N 71 DC "O5'" O N N 72 DC "C5'" C N N 73 DC "C4'" C N R 74 DC "O4'" O N N 75 DC "C3'" C N S 76 DC "O3'" O N N 77 DC "C2'" C N N 78 DC "C1'" C N R 79 DC N1 N N N 80 DC C2 C N N 81 DC O2 O N N 82 DC N3 N N N 83 DC C4 C N N 84 DC N4 N N N 85 DC C5 C N N 86 DC C6 C N N 87 DC HOP3 H N N 88 DC HOP2 H N N 89 DC "H5'" H N N 90 DC "H5''" H N N 91 DC "H4'" H N N 92 DC "H3'" H N N 93 DC "HO3'" H N N 94 DC "H2'" H N N 95 DC "H2''" H N N 96 DC "H1'" H N N 97 DC H41 H N N 98 DC H42 H N N 99 DC H5 H N N 100 DC H6 H N N 101 DT OP3 O N N 102 DT P P N N 103 DT OP1 O N N 104 DT OP2 O N N 105 DT "O5'" O N N 106 DT "C5'" C N N 107 DT "C4'" C N R 108 DT "O4'" O N N 109 DT "C3'" C N S 110 DT "O3'" O N N 111 DT "C2'" C N N 112 DT "C1'" C N R 113 DT N1 N N N 114 DT C2 C N N 115 DT O2 O N N 116 DT N3 N N N 117 DT C4 C N N 118 DT O4 O N N 119 DT C5 C N N 120 DT C7 C N N 121 DT C6 C N N 122 DT HOP3 H N N 123 DT HOP2 H N N 124 DT "H5'" H N N 125 DT "H5''" H N N 126 DT "H4'" H N N 127 DT "H3'" H N N 128 DT "HO3'" H N N 129 DT "H2'" H N N 130 DT "H2''" H N N 131 DT "H1'" H N N 132 DT H3 H N N 133 DT H71 H N N 134 DT H72 H N N 135 DT H73 H N N 136 DT H6 H N N 137 GF2 F F N N 138 GF2 P P N N 139 GF2 N1 N N N 140 GF2 C2 C N N 141 GF2 N2 N N N 142 GF2 N3 N N N 143 GF2 C4 C Y N 144 GF2 C5 C Y N 145 GF2 C6 C N N 146 GF2 O6 O N N 147 GF2 N7 N Y N 148 GF2 C8 C Y N 149 GF2 N9 N Y N 150 GF2 "C1'" C N R 151 GF2 OP2 O N N 152 GF2 "C2'" C N R 153 GF2 OP1 O N N 154 GF2 "C3'" C N R 155 GF2 "O3'" O N N 156 GF2 "C4'" C N R 157 GF2 "O4'" O N N 158 GF2 "C5'" C N N 159 GF2 "O5'" O N N 160 GF2 OP3 O N N 161 GF2 HN1 H N N 162 GF2 HN2 H N N 163 GF2 HN2A H N N 164 GF2 H8 H N N 165 GF2 "H1'" H N N 166 GF2 HOP2 H N N 167 GF2 "H2'" H N N 168 GF2 "H3'" H N N 169 GF2 "HO3'" H N N 170 GF2 "H4'" H N N 171 GF2 "H5'" H N N 172 GF2 "H5'A" H N N 173 GF2 HOP3 H N N 174 # 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 3D1 "O5'" "C5'" sing N N 1 3D1 "O5'" "H5'" sing N N 2 3D1 "C5'" "C4'" sing N N 3 3D1 "C5'" "H5'1" sing N N 4 3D1 "C5'" "H5'2" sing N N 5 3D1 "C4'" "O4'" sing N N 6 3D1 "C4'" "C3'" sing N N 7 3D1 "C4'" "H4'" sing N N 8 3D1 "O4'" "C1'" sing N N 9 3D1 "C1'" N9 sing N N 10 3D1 "C1'" "C2'" sing N N 11 3D1 "C1'" "H1'" sing N N 12 3D1 N9 C4 sing Y N 13 3D1 N9 C8 sing Y N 14 3D1 C4 N3 doub Y N 15 3D1 C4 C5 sing Y N 16 3D1 N3 C2 sing Y N 17 3D1 C2 N1 doub Y N 18 3D1 C2 H2 sing N N 19 3D1 N1 C6 sing Y N 20 3D1 C6 N6 sing N N 21 3D1 C6 C5 doub Y N 22 3D1 N6 HN61 sing N N 23 3D1 N6 HN62 sing N N 24 3D1 C5 N7 sing Y N 25 3D1 N7 C8 doub Y N 26 3D1 C8 H8 sing N N 27 3D1 "C2'" "C3'" sing N N 28 3D1 "C2'" "H2'1" sing N N 29 3D1 "C2'" "H2'2" sing N N 30 3D1 "C3'" "O3'" sing N N 31 3D1 "C3'" "H3'" sing N N 32 3D1 "O3'" H1 sing N N 33 DA OP3 P sing N N 34 DA OP3 HOP3 sing N N 35 DA P OP1 doub N N 36 DA P OP2 sing N N 37 DA P "O5'" sing N N 38 DA OP2 HOP2 sing N N 39 DA "O5'" "C5'" sing N N 40 DA "C5'" "C4'" sing N N 41 DA "C5'" "H5'" sing N N 42 DA "C5'" "H5''" sing N N 43 DA "C4'" "O4'" sing N N 44 DA "C4'" "C3'" sing N N 45 DA "C4'" "H4'" sing N N 46 DA "O4'" "C1'" sing N N 47 DA "C3'" "O3'" sing N N 48 DA "C3'" "C2'" sing N N 49 DA "C3'" "H3'" sing N N 50 DA "O3'" "HO3'" sing N N 51 DA "C2'" "C1'" sing N N 52 DA "C2'" "H2'" sing N N 53 DA "C2'" "H2''" sing N N 54 DA "C1'" N9 sing N N 55 DA "C1'" "H1'" sing N N 56 DA N9 C8 sing Y N 57 DA N9 C4 sing Y N 58 DA C8 N7 doub Y N 59 DA C8 H8 sing N N 60 DA N7 C5 sing Y N 61 DA C5 C6 sing Y N 62 DA C5 C4 doub Y N 63 DA C6 N6 sing N N 64 DA C6 N1 doub Y N 65 DA N6 H61 sing N N 66 DA N6 H62 sing N N 67 DA N1 C2 sing Y N 68 DA C2 N3 doub Y N 69 DA C2 H2 sing N N 70 DA N3 C4 sing Y N 71 DC OP3 P sing N N 72 DC OP3 HOP3 sing N N 73 DC P OP1 doub N N 74 DC P OP2 sing N N 75 DC P "O5'" sing N N 76 DC OP2 HOP2 sing N N 77 DC "O5'" "C5'" sing N N 78 DC "C5'" "C4'" sing N N 79 DC "C5'" "H5'" sing N N 80 DC "C5'" "H5''" sing N N 81 DC "C4'" "O4'" sing N N 82 DC "C4'" "C3'" sing N N 83 DC "C4'" "H4'" sing N N 84 DC "O4'" "C1'" sing N N 85 DC "C3'" "O3'" sing N N 86 DC "C3'" "C2'" sing N N 87 DC "C3'" "H3'" sing N N 88 DC "O3'" "HO3'" sing N N 89 DC "C2'" "C1'" sing N N 90 DC "C2'" "H2'" sing N N 91 DC "C2'" "H2''" sing N N 92 DC "C1'" N1 sing N N 93 DC "C1'" "H1'" sing N N 94 DC N1 C2 sing N N 95 DC N1 C6 sing N N 96 DC C2 O2 doub N N 97 DC C2 N3 sing N N 98 DC N3 C4 doub N N 99 DC C4 N4 sing N N 100 DC C4 C5 sing N N 101 DC N4 H41 sing N N 102 DC N4 H42 sing N N 103 DC C5 C6 doub N N 104 DC C5 H5 sing N N 105 DC C6 H6 sing N N 106 DT OP3 P sing N N 107 DT OP3 HOP3 sing N N 108 DT P OP1 doub N N 109 DT P OP2 sing N N 110 DT P "O5'" sing N N 111 DT OP2 HOP2 sing N N 112 DT "O5'" "C5'" sing N N 113 DT "C5'" "C4'" sing N N 114 DT "C5'" "H5'" sing N N 115 DT "C5'" "H5''" sing N N 116 DT "C4'" "O4'" sing N N 117 DT "C4'" "C3'" sing N N 118 DT "C4'" "H4'" sing N N 119 DT "O4'" "C1'" sing N N 120 DT "C3'" "O3'" sing N N 121 DT "C3'" "C2'" sing N N 122 DT "C3'" "H3'" sing N N 123 DT "O3'" "HO3'" sing N N 124 DT "C2'" "C1'" sing N N 125 DT "C2'" "H2'" sing N N 126 DT "C2'" "H2''" sing N N 127 DT "C1'" N1 sing N N 128 DT "C1'" "H1'" sing N N 129 DT N1 C2 sing N N 130 DT N1 C6 sing N N 131 DT C2 O2 doub N N 132 DT C2 N3 sing N N 133 DT N3 C4 sing N N 134 DT N3 H3 sing N N 135 DT C4 O4 doub N N 136 DT C4 C5 sing N N 137 DT C5 C7 sing N N 138 DT C5 C6 doub N N 139 DT C7 H71 sing N N 140 DT C7 H72 sing N N 141 DT C7 H73 sing N N 142 DT C6 H6 sing N N 143 GF2 P "O5'" sing N N 144 GF2 N1 C2 sing N N 145 GF2 C2 N3 doub N N 146 GF2 C2 N2 sing N N 147 GF2 C4 N3 sing N N 148 GF2 C5 C4 doub Y N 149 GF2 C6 N1 sing N N 150 GF2 C6 C5 sing N N 151 GF2 O6 C6 doub N N 152 GF2 N7 C5 sing Y N 153 GF2 N7 C8 doub Y N 154 GF2 C8 N9 sing Y N 155 GF2 N9 C4 sing Y N 156 GF2 N9 "C1'" sing N N 157 GF2 "C1'" "O4'" sing N N 158 GF2 OP2 P sing N N 159 GF2 "C2'" F sing N N 160 GF2 "C2'" "C1'" sing N N 161 GF2 OP1 P doub N N 162 GF2 "C3'" "C2'" sing N N 163 GF2 "C3'" "C4'" sing N N 164 GF2 "O3'" "C3'" sing N N 165 GF2 "C4'" "O4'" sing N N 166 GF2 "C5'" "C4'" sing N N 167 GF2 "O5'" "C5'" sing N N 168 GF2 P OP3 sing N N 169 GF2 N1 HN1 sing N N 170 GF2 N2 HN2 sing N N 171 GF2 N2 HN2A sing N N 172 GF2 C8 H8 sing N N 173 GF2 "C1'" "H1'" sing N N 174 GF2 OP2 HOP2 sing N N 175 GF2 "C2'" "H2'" sing N N 176 GF2 "C3'" "H3'" sing N N 177 GF2 "O3'" "HO3'" sing N N 178 GF2 "C4'" "H4'" sing N N 179 GF2 "C5'" "H5'" sing N N 180 GF2 "C5'" "H5'A" sing N N 181 GF2 OP3 HOP3 sing N N 182 # _ndb_struct_conf_na.entry_id 8Y1I _ndb_struct_conf_na.feature '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 DA 2 1_555 B DT 7 1_555 0.028 -0.102 0.258 9.106 -14.044 -5.259 1 A_DA2:DT15_B A 2 ? B 15 ? 20 1 1 A DC 3 1_555 B GF2 6 1_555 0.306 -0.197 -0.316 -11.217 2.593 -2.775 2 A_DC3:GF214_B A 3 ? B 14 ? 19 1 1 A DC 4 1_555 B GF2 5 1_555 0.276 -0.133 0.360 -18.352 -2.370 -3.309 3 A_DC4:GF213_B A 4 ? B 13 ? 19 1 1 A GF2 5 1_555 B DC 4 1_555 -0.295 -0.132 0.205 20.211 -3.882 -2.426 4 A_GF25:DC12_B A 5 ? B 12 ? 19 1 1 A GF2 6 1_555 B DC 3 1_555 -0.316 -0.198 -0.320 11.325 -0.337 -2.361 5 A_GF26:DC11_B A 6 ? B 11 ? 19 1 1 A DT 7 1_555 B DA 2 1_555 -0.046 -0.103 0.354 -11.023 -13.969 -5.649 6 A_DT7:DA10_B A 7 ? B 10 ? 20 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 DA 2 1_555 B DT 7 1_555 A DC 3 1_555 B GF2 6 1_555 0.158 -0.506 4.828 -4.087 -7.768 38.559 0.613 -0.950 4.796 -11.581 6.092 39.508 1 AA_DA2DC3:GF214DT15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DC 3 1_555 B GF2 6 1_555 A DC 4 1_555 B GF2 5 1_555 0.202 -0.595 4.034 -0.661 30.110 26.555 -4.954 -0.386 2.269 49.503 1.086 39.948 2 AA_DC3DC4:GF213GF214_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DC 4 1_555 B GF2 5 1_555 A GF2 5 1_555 B DC 4 1_555 0.203 0.860 2.730 1.574 -10.748 32.242 2.842 -0.146 2.339 -18.703 -2.738 33.977 3 AA_DC4GF25:DC12GF213_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A GF2 5 1_555 B DC 4 1_555 A GF2 6 1_555 B DC 3 1_555 -0.131 -0.618 4.087 0.394 30.079 26.502 -5.044 0.246 2.288 49.531 -0.649 39.887 4 AA_GF25GF26:DC11DC12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A GF2 6 1_555 B DC 3 1_555 A DT 7 1_555 B DA 2 1_555 -0.162 -0.604 4.788 3.603 -6.337 37.064 0.275 0.937 4.787 -9.852 -5.602 37.750 5 AA_GF26DT7:DA10DC11_BB A 6 ? B 11 ? A 7 ? B 10 ? # _pdbx_audit_support.funding_organization 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'Direct Drive' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Agilent _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 8Y1I _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C F H N O P # loop_ #