data_6JWD # _entry.id 6JWD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 6JWD pdb_00006jwd 10.2210/pdb6jwd/pdb WWPDB D_1300011902 ? ? BMRB 36246 ? 10.13018/BMR36246 # 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 2020-04-22 2 'Structure model' 1 1 2023-06-14 3 'Structure model' 1 2 2024-05-15 # _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' 'Database references' 2 2 'Structure model' Other 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 6JWD _pdbx_database_status.recvd_initial_deposition_date 2019-04-19 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type BMRB 'the chemical shifts of free RET G-quadruplex' 17397 unspecified PDB 'the free RET G-quadruplex structure' 2L88 unspecified BMRB ;structure of RET G-quadruplex in complex with berberine ; 36246 unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Wang, F.' 1 ? 'Wang, C.' 2 ? 'Liu, Y.' 3 ? 'Lan, W.X.' 4 ? 'Li, Y.M.' 5 ? 'Wang, R.X.' 6 ? 'Cao, C.' 7 ? # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary 'Chem.Commun.(Camb.)' ? ? 1364-548X ? ? 56 ? 2099 2102 'Colchicine selective interaction with oncogene RET G-quadruplex revealed by NMR.' 2020 ? 10.1039/d0cc00221f 32025680 ? ? ? ? ? ? ? ? UK ? ? 1 'Nucleic Acids Res.' NARHAD 0389 1362-4962 ? ? 39 ? 6753 6763 'Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence.' 2011 ? 10.1093/nar/gkr233 21540209 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, F.' 1 ? primary 'Wang, C.' 2 ? primary 'Liu, Y.' 3 ? primary 'Lan, W.' 4 ? primary 'Han, H.' 5 ? primary 'Wang, R.' 6 ? primary 'Huang, S.' 7 ? primary 'Cao, C.' 8 0000-0001-7865-8249 1 'Tong, X.' 9 ? 1 'Lan, W.' 10 ? 1 'Zhang, X.' 11 ? 1 'Wu, H.' 12 ? 1 'Liu, M.' 13 ? 1 'Cao, C.' 14 ? # 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 (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3') ; 6394.074 1 ? ? ? ? 2 non-polymer syn BERBERINE 336.361 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DG)(DG)(DC)(DG)(DG)(DG)(DG)(DC)(DG)(DG)(DG)(DG)(DC)(DG)(DG)(DG)(DG)(DT)' _entity_poly.pdbx_seq_one_letter_code_can GGGGCGGGGCGGGGCGGGGT _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name BERBERINE _pdbx_entity_nonpoly.comp_id BER # 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 DG n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DG n 1 8 DG n 1 9 DG n 1 10 DC n 1 11 DG n 1 12 DG n 1 13 DG n 1 14 DG n 1 15 DC n 1 16 DG n 1 17 DG n 1 18 DG n 1 19 DG n 1 20 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 20 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _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 BER non-polymer . BERBERINE ? 'C20 H18 N O4 1' 336.361 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 DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DG 13 13 13 DG DG A . n A 1 14 DG 14 14 14 DG DG A . n A 1 15 DC 15 15 15 DC DC A . n A 1 16 DG 16 16 16 DG DG A . n A 1 17 DG 17 17 17 DG DG A . n A 1 18 DG 18 18 18 DG DG A . n A 1 19 DG 19 19 19 DG DG A . n A 1 20 DT 20 20 20 DT DT A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id BER _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 101 _pdbx_nonpoly_scheme.pdb_mon_id BER _pdbx_nonpoly_scheme.auth_mon_id BER _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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 6JWD _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6JWD _struct.title 'structure of RET G-quadruplex in complex with berberine' _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 6JWD _struct_keywords.text 'RET, G-quadruplex, berberine, 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 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6JWD _struct_ref.pdbx_db_accession 6JWD _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6JWD _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 20 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6JWD _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 20 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 600 ? 1 MORE 5 ? 1 'SSA (A^2)' 3640 ? # _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 none _pdbx_struct_assembly_auth_evidence.details 'one-dimensional NMR detected the Hoogsteen hydrogen bonds formed in G-quadruplex' # _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 ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 hydrog1 hydrog ? ? A DG 1 N7 ? ? ? 1_555 A DG 7 N2 ? ? A DG 1 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DG 7 N1 ? ? A DG 1 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DG 17 O6 ? ? A DG 1 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DG 17 N7 ? ? A DG 1 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DG 8 O6 ? ? A DG 2 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 8 N7 ? ? A DG 2 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 2 N7 ? ? ? 1_555 A DG 18 N2 ? ? A DG 2 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DG 18 N1 ? ? A DG 2 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DG 9 O6 ? ? A DG 3 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 9 N7 ? ? A DG 3 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 3 N7 ? ? ? 1_555 A DG 19 N2 ? ? A DG 3 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DG 19 N1 ? ? A DG 3 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 7 N7 ? ? ? 1_555 A DG 11 N2 ? ? A DG 7 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DG 11 N1 ? ? A DG 7 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DG 12 O6 ? ? A DG 8 A DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DG 12 N7 ? ? A DG 8 A DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DG 13 O6 ? ? A DG 9 A DG 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DG 13 N7 ? ? A DG 9 A DG 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DG 11 N7 ? ? ? 1_555 A DG 17 N2 ? ? A DG 11 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A DG 11 O6 ? ? ? 1_555 A DG 17 N1 ? ? A DG 11 A DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? A DG 12 N1 ? ? ? 1_555 A DG 18 O6 ? ? A DG 12 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A DG 12 N2 ? ? ? 1_555 A DG 18 N7 ? ? A DG 12 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? A DG 13 N1 ? ? ? 1_555 A DG 19 O6 ? ? A DG 13 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? A DG 13 N2 ? ? ? 1_555 A DG 19 N7 ? ? A DG 13 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id BER _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'binding site for residue BER A 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DG A 3 ? DG A 3 . ? 1_555 ? 2 AC1 6 DG A 13 ? DG A 13 . ? 1_555 ? 3 AC1 6 DG A 14 ? DG A 14 . ? 1_555 ? 4 AC1 6 DG A 16 ? DG A 16 . ? 1_555 ? 5 AC1 6 DG A 19 ? DG A 19 . ? 1_555 ? 6 AC1 6 DT A 20 ? DT A 20 . ? 1_555 ? # 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 2 "H3'" A DG 16 ? ? OP2 A DG 18 ? ? 1.59 2 6 "H3'" A DG 16 ? ? OP2 A DG 18 ? ? 1.51 3 8 "H3'" A DG 16 ? ? OP2 A DG 18 ? ? 1.58 4 9 "H3'" A DG 16 ? ? OP2 A DG 18 ? ? 1.59 5 12 "H3'" A DG 16 ? ? OP2 A DG 18 ? ? 1.59 # 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 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.83 110.10 -8.27 1.00 N 2 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.19 108.30 1.89 0.30 N 3 2 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.27 110.10 -8.83 1.00 N 4 2 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.14 108.30 1.84 0.30 N 5 3 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.36 110.10 -8.74 1.00 N 6 3 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.18 108.30 1.88 0.30 N 7 4 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.19 110.10 -8.91 1.00 N 8 4 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.16 108.30 1.86 0.30 N 9 5 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.79 110.10 -7.31 1.00 N 10 5 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.14 108.30 1.84 0.30 N 11 6 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.26 110.10 -7.84 1.00 N 12 6 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.10 108.30 1.80 0.30 N 13 7 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.19 110.10 -6.91 1.00 N 14 7 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.11 108.30 1.81 0.30 N 15 8 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.25 110.10 -7.85 1.00 N 16 8 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.21 108.30 1.91 0.30 N 17 9 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.87 110.10 -7.23 1.00 N 18 9 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.21 108.30 1.91 0.30 N 19 10 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.22 110.10 -6.88 1.00 N 20 10 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.16 108.30 1.86 0.30 N 21 11 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.01 110.10 -7.09 1.00 N 22 11 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.16 108.30 1.86 0.30 N 23 12 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.92 110.10 -8.18 1.00 N 24 12 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.17 108.30 1.87 0.30 N 25 13 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.13 110.10 -6.97 1.00 N 26 13 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.13 108.30 1.83 0.30 N 27 14 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.88 110.10 -8.22 1.00 N 28 14 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.17 108.30 1.87 0.30 N 29 15 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.44 110.10 -7.66 1.00 N 30 15 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.15 108.30 1.85 0.30 N 31 16 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.31 110.10 -7.79 1.00 N 32 16 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.15 108.30 1.85 0.30 N 33 17 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.83 110.10 -8.27 1.00 N 34 17 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.13 108.30 1.83 0.30 N 35 18 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 102.41 110.10 -7.69 1.00 N 36 18 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.17 108.30 1.87 0.30 N 37 19 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.87 110.10 -8.23 1.00 N 38 19 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.17 108.30 1.87 0.30 N 39 20 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 101.69 110.10 -8.41 1.00 N 40 20 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.13 108.30 1.83 0.30 N # _pdbx_entry_details.entry_id 6JWD _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_nmr_ensemble.entry_id 6JWD _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 6JWD _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 '1.4 mM RET G4-DNA, 1.68 mM BERBERINE, 20 mM Potassium Phosphate Monobasic, 80 mM potassium chloride, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label 'RET G4-DNA sample' _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 'RET G4-DNA' 1.4 ? mM 'natural abundance' 1 BERBERINE 1.68 ? mM 'natural abundance' 1 'Potassium Phosphate Monobasic' 20 ? mM 'natural abundance' 1 'potassium chloride' 80 ? 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 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength 100 _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 'RET G4 berberine solution complex' _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 TOCSY' 1 anisotropic 3 1 1 '2D 1H-1H COSY' 1 anisotropic # _pdbx_nmr_refine.entry_id 6JWD _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 3 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 processing NMRDraw ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 2 'chemical shift assignment' Sparky ? Goddard 3 'structure calculation' '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 BER C1 C Y N 1 BER C2 C Y N 2 BER N1 N Y N 3 BER C3 C Y N 4 BER C4 C Y N 5 BER C5 C Y N 6 BER C6 C Y N 7 BER C7 C N N 8 BER C8 C Y N 9 BER C9 C Y N 10 BER C10 C N N 11 BER C11 C Y N 12 BER C12 C Y N 13 BER C13 C Y N 14 BER C14 C Y N 15 BER O1 O N N 16 BER C15 C Y N 17 BER C16 C Y N 18 BER O2 O N N 19 BER C17 C N N 20 BER C18 C Y N 21 BER O3 O N N 22 BER O4 O N N 23 BER C19 C N N 24 BER C20 C N N 25 BER H31 H N N 26 BER H51 H N N 27 BER H61 H N N 28 BER H71 H N N 29 BER H72 H N N 30 BER H91 H N N 31 BER H101 H N N 32 BER H102 H N N 33 BER H131 H N N 34 BER H161 H N N 35 BER H171 H N N 36 BER H172 H N N 37 BER H191 H N N 38 BER H192 H N N 39 BER H193 H N N 40 BER H201 H N N 41 BER H202 H N N 42 BER H203 H N N 43 DC OP3 O N N 44 DC P P N N 45 DC OP1 O N N 46 DC OP2 O N N 47 DC "O5'" O N N 48 DC "C5'" C N N 49 DC "C4'" C N R 50 DC "O4'" O N N 51 DC "C3'" C N S 52 DC "O3'" O N N 53 DC "C2'" C N N 54 DC "C1'" C N R 55 DC N1 N N N 56 DC C2 C N N 57 DC O2 O N N 58 DC N3 N N N 59 DC C4 C N N 60 DC N4 N N N 61 DC C5 C N N 62 DC C6 C N N 63 DC HOP3 H N N 64 DC HOP2 H N N 65 DC "H5'" H N N 66 DC "H5''" H N N 67 DC "H4'" H N N 68 DC "H3'" H N N 69 DC "HO3'" H N N 70 DC "H2'" H N N 71 DC "H2''" H N N 72 DC "H1'" H N N 73 DC H41 H N N 74 DC H42 H N N 75 DC H5 H N N 76 DC H6 H N N 77 DG OP3 O N N 78 DG P P N N 79 DG OP1 O N N 80 DG OP2 O N N 81 DG "O5'" O N N 82 DG "C5'" C N N 83 DG "C4'" C N R 84 DG "O4'" O N N 85 DG "C3'" C N S 86 DG "O3'" O N N 87 DG "C2'" C N N 88 DG "C1'" C N R 89 DG N9 N Y N 90 DG C8 C Y N 91 DG N7 N Y N 92 DG C5 C Y N 93 DG C6 C N N 94 DG O6 O N N 95 DG N1 N N N 96 DG C2 C N N 97 DG N2 N N N 98 DG N3 N N N 99 DG C4 C Y N 100 DG HOP3 H N N 101 DG HOP2 H N N 102 DG "H5'" H N N 103 DG "H5''" H N N 104 DG "H4'" H N N 105 DG "H3'" H N N 106 DG "HO3'" H N N 107 DG "H2'" H N N 108 DG "H2''" H N N 109 DG "H1'" H N N 110 DG H8 H N N 111 DG H1 H N N 112 DG H21 H N N 113 DG H22 H N N 114 DT OP3 O N N 115 DT P P N N 116 DT OP1 O N N 117 DT OP2 O N N 118 DT "O5'" O N N 119 DT "C5'" C N N 120 DT "C4'" C N R 121 DT "O4'" O N N 122 DT "C3'" C N S 123 DT "O3'" O N N 124 DT "C2'" C N N 125 DT "C1'" C N R 126 DT N1 N N N 127 DT C2 C N N 128 DT O2 O N N 129 DT N3 N N N 130 DT C4 C N N 131 DT O4 O N N 132 DT C5 C N N 133 DT C7 C N N 134 DT C6 C N N 135 DT HOP3 H N N 136 DT HOP2 H N N 137 DT "H5'" H N N 138 DT "H5''" H N N 139 DT "H4'" H N N 140 DT "H3'" H N N 141 DT "HO3'" H N N 142 DT "H2'" H N N 143 DT "H2''" H N N 144 DT "H1'" H N N 145 DT H3 H N N 146 DT H71 H N N 147 DT H72 H N N 148 DT H73 H N N 149 DT H6 H N N 150 # 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 BER C1 C2 sing Y N 1 BER C1 N1 doub Y N 2 BER C1 C3 sing Y N 3 BER C2 C4 doub Y N 4 BER C2 C5 sing Y N 5 BER N1 C6 sing Y N 6 BER N1 C7 sing N N 7 BER C3 C8 doub Y N 8 BER C3 H31 sing N N 9 BER C4 C9 sing Y N 10 BER C4 C10 sing N N 11 BER C5 C11 doub Y N 12 BER C5 H51 sing N N 13 BER C6 C12 doub Y N 14 BER C6 H61 sing N N 15 BER C7 C10 sing N N 16 BER C7 H71 sing N N 17 BER C7 H72 sing N N 18 BER C8 C12 sing Y N 19 BER C8 C13 sing Y N 20 BER C9 C14 doub Y N 21 BER C9 H91 sing N N 22 BER C10 H101 sing N N 23 BER C10 H102 sing N N 24 BER C11 C14 sing Y N 25 BER C11 O1 sing N N 26 BER C12 C15 sing Y N 27 BER C13 C16 doub Y N 28 BER C13 H131 sing N N 29 BER C14 O2 sing N N 30 BER O1 C17 sing N N 31 BER C15 C18 doub Y N 32 BER C15 O3 sing N N 33 BER C16 C18 sing Y N 34 BER C16 H161 sing N N 35 BER O2 C17 sing N N 36 BER C17 H171 sing N N 37 BER C17 H172 sing N N 38 BER C18 O4 sing N N 39 BER O3 C19 sing N N 40 BER O4 C20 sing N N 41 BER C19 H191 sing N N 42 BER C19 H192 sing N N 43 BER C19 H193 sing N N 44 BER C20 H201 sing N N 45 BER C20 H202 sing N N 46 BER C20 H203 sing N N 47 DC OP3 P sing N N 48 DC OP3 HOP3 sing N N 49 DC P OP1 doub N N 50 DC P OP2 sing N N 51 DC P "O5'" sing N N 52 DC OP2 HOP2 sing N N 53 DC "O5'" "C5'" sing N N 54 DC "C5'" "C4'" sing N N 55 DC "C5'" "H5'" sing N N 56 DC "C5'" "H5''" sing N N 57 DC "C4'" "O4'" sing N N 58 DC "C4'" "C3'" sing N N 59 DC "C4'" "H4'" sing N N 60 DC "O4'" "C1'" sing N N 61 DC "C3'" "O3'" sing N N 62 DC "C3'" "C2'" sing N N 63 DC "C3'" "H3'" sing N N 64 DC "O3'" "HO3'" sing N N 65 DC "C2'" "C1'" sing N N 66 DC "C2'" "H2'" sing N N 67 DC "C2'" "H2''" sing N N 68 DC "C1'" N1 sing N N 69 DC "C1'" "H1'" sing N N 70 DC N1 C2 sing N N 71 DC N1 C6 sing N N 72 DC C2 O2 doub N N 73 DC C2 N3 sing N N 74 DC N3 C4 doub N N 75 DC C4 N4 sing N N 76 DC C4 C5 sing N N 77 DC N4 H41 sing N N 78 DC N4 H42 sing N N 79 DC C5 C6 doub N N 80 DC C5 H5 sing N N 81 DC C6 H6 sing N N 82 DG OP3 P sing N N 83 DG OP3 HOP3 sing N N 84 DG P OP1 doub N N 85 DG P OP2 sing N N 86 DG P "O5'" sing N N 87 DG OP2 HOP2 sing N N 88 DG "O5'" "C5'" sing N N 89 DG "C5'" "C4'" sing N N 90 DG "C5'" "H5'" sing N N 91 DG "C5'" "H5''" sing N N 92 DG "C4'" "O4'" sing N N 93 DG "C4'" "C3'" sing N N 94 DG "C4'" "H4'" sing N N 95 DG "O4'" "C1'" sing N N 96 DG "C3'" "O3'" sing N N 97 DG "C3'" "C2'" sing N N 98 DG "C3'" "H3'" sing N N 99 DG "O3'" "HO3'" sing N N 100 DG "C2'" "C1'" sing N N 101 DG "C2'" "H2'" sing N N 102 DG "C2'" "H2''" sing N N 103 DG "C1'" N9 sing N N 104 DG "C1'" "H1'" sing N N 105 DG N9 C8 sing Y N 106 DG N9 C4 sing Y N 107 DG C8 N7 doub Y N 108 DG C8 H8 sing N N 109 DG N7 C5 sing Y N 110 DG C5 C6 sing N N 111 DG C5 C4 doub Y N 112 DG C6 O6 doub N N 113 DG C6 N1 sing N N 114 DG N1 C2 sing N N 115 DG N1 H1 sing N N 116 DG C2 N2 sing N N 117 DG C2 N3 doub N N 118 DG N2 H21 sing N N 119 DG N2 H22 sing N N 120 DG N3 C4 sing N N 121 DT OP3 P sing N N 122 DT OP3 HOP3 sing N N 123 DT P OP1 doub N N 124 DT P OP2 sing N N 125 DT P "O5'" sing N N 126 DT OP2 HOP2 sing N N 127 DT "O5'" "C5'" sing N N 128 DT "C5'" "C4'" sing N N 129 DT "C5'" "H5'" sing N N 130 DT "C5'" "H5''" sing N N 131 DT "C4'" "O4'" sing N N 132 DT "C4'" "C3'" sing N N 133 DT "C4'" "H4'" sing N N 134 DT "O4'" "C1'" sing N N 135 DT "C3'" "O3'" sing N N 136 DT "C3'" "C2'" sing N N 137 DT "C3'" "H3'" sing N N 138 DT "O3'" "HO3'" sing N N 139 DT "C2'" "C1'" sing N N 140 DT "C2'" "H2'" sing N N 141 DT "C2'" "H2''" sing N N 142 DT "C1'" N1 sing N N 143 DT "C1'" "H1'" sing N N 144 DT N1 C2 sing N N 145 DT N1 C6 sing N N 146 DT C2 O2 doub N N 147 DT C2 N3 sing N N 148 DT N3 C4 sing N N 149 DT N3 H3 sing N N 150 DT C4 O4 doub N N 151 DT C4 C5 sing N N 152 DT C5 C7 sing N N 153 DT C5 C6 doub N N 154 DT C7 H71 sing N N 155 DT C7 H72 sing N N 156 DT C7 H73 sing N N 157 DT C6 H6 sing N N 158 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6JWD 'double helix' 6JWD 'z-form double helix' 6JWD 'quadruple 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 A DG 7 1_555 -1.222 -3.690 -0.023 -1.137 1.360 94.042 1 A_DG1:DG7_A A 1 ? A 7 ? 6 3 1 A DG 17 1_555 A DG 11 1_555 1.307 3.680 0.168 -7.118 -8.965 -91.863 2 A_DG17:DG11_A A 17 ? A 11 ? 6 3 1 A DG 18 1_555 A DG 2 1_555 1.763 3.504 -0.121 -4.475 2.428 -89.755 3 A_DG18:DG2_A A 18 ? A 2 ? 6 3 1 A DG 9 1_555 A DG 13 1_555 -2.488 3.079 0.165 9.691 6.249 83.731 4 A_DG9:DG13_A A 9 ? A 13 ? 6 3 1 A DG 3 1_555 A DG 19 1_555 2.360 -3.245 0.266 -3.975 1.465 -84.625 5 A_DG3:DG19_A A 3 ? A 19 ? 6 3 1 A DG 8 1_555 A DG 12 1_555 -1.710 3.489 0.493 2.128 1.799 89.945 6 A_DG8:DG12_A A 8 ? A 12 ? 6 3 # 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 A DG 7 1_555 A DG 17 1_555 A DG 11 1_555 2.043 3.419 -0.061 -1.748 0.886 -179.603 -1.709 1.022 -0.061 -0.443 -0.874 -179.603 1 AA_DG1DG17:DG11DG7_AA A 1 ? A 7 ? A 17 ? A 11 ? 1 A DG 17 1_555 A DG 11 1_555 A DG 18 1_555 A DG 2 1_555 -5.106 -2.196 -0.538 -55.621 -167.266 163.721 -1.116 2.559 -0.009 -83.651 27.816 179.472 2 AA_DG17DG18:DG2DG11_AA A 17 ? A 11 ? A 18 ? A 2 ? 1 A DG 9 1_555 A DG 13 1_555 A DG 3 1_555 A DG 19 1_555 0.938 -3.686 0.480 -2.722 -0.987 -178.775 1.843 0.469 0.480 0.493 -1.361 -178.775 3 AA_DG9DG3:DG19DG13_AA A 9 ? A 13 ? A 3 ? A 19 ? 1 A DG 3 1_555 A DG 19 1_555 A DG 8 1_555 A DG 12 1_555 1.343 -3.659 3.941 -0.782 1.263 -154.884 1.869 0.685 3.952 -0.647 -0.401 -154.886 4 AA_DG3DG8:DG12DG19_AA A 3 ? A 19 ? A 8 ? A 12 ? # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id BER _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id BER _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 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Agilent _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 6JWD _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.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 H N O P # loop_