data_6K3Y # _entry.id 6K3Y # _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 6K3Y pdb_00006k3y 10.2210/pdb6k3y/pdb WWPDB D_1300010070 ? ? BMRB 36253 ? 10.13018/BMR36253 # 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 2020-01-15 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 2 'Structure model' 'Structure summary' 4 3 'Structure model' 'Data collection' 5 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' chem_comp 2 2 'Structure model' database_2 3 2 'Structure model' pdbx_database_status 4 3 'Structure model' chem_comp_atom 5 3 'Structure model' chem_comp_bond 6 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' '_chem_comp.pdbx_synonyms' 2 2 'Structure model' '_database_2.pdbx_DOI' 3 2 'Structure model' '_database_2.pdbx_database_accession' 4 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 5 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 6K3Y _pdbx_database_status.recvd_initial_deposition_date 2019-05-22 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # _pdbx_database_related.db_name BMRB _pdbx_database_related.details ;G-quadruplex complex with cyclic dinucleotide 3'-3' cGAMP ; _pdbx_database_related.db_id 36253 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Winnerdy, F.R.' 1 0000-0002-5010-4719 'Heddi, B.' 2 0000-0002-5535-6237 'Phan, A.T.' 3 0000-0002-4970-3861 # _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 J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 141 _citation.language ? _citation.page_first 18038 _citation.page_last 18047 _citation.title 'Solution Structures of a G-Quadruplex Bound to Linear- and Cyclic-Dinucleotides.' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.9b05642 _citation.pdbx_database_id_PubMed 31661272 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Winnerdy, F.R.' 1 ? primary 'Das, P.' 2 ? primary 'Heddi, B.' 3 ? primary 'Phan, A.T.' 4 0000-0002-4970-3861 # 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(*TP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') ; 5401.463 1 ? ? ? ? 2 non-polymer syn ;2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one ; 674.411 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name delta1 # _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 '(DT)(DT)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)' _entity_poly.pdbx_seq_one_letter_code_can TTGGTGGGTGGGTGGGT _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name ;2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one ; _pdbx_entity_nonpoly.comp_id 4BW # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 DG n 1 7 DG n 1 8 DG n 1 9 DT n 1 10 DG n 1 11 DG n 1 12 DG n 1 13 DT n 1 14 DG n 1 15 DG n 1 16 DG n 1 17 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 17 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _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 4BW non-polymer . ;2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one ; ;3',3' cGAMP; c-GMP-AMP; c[G(3',5')pA(3',5')p] ; 'C20 H24 N10 O13 P2' 674.411 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 DT 1 1 1 DT DT A . n A 1 2 DT 2 2 2 DT DT 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 DT 5 5 5 DT DT 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 DT 9 9 9 DT DT A . n A 1 10 DG 10 10 10 DG DG 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 DT 13 13 13 DT DT A . n A 1 14 DG 14 14 14 DG DG A . n A 1 15 DG 15 15 15 DG DG A . n A 1 16 DG 16 16 16 DG DG A . n A 1 17 DT 17 17 17 DT DT A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 4BW _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 4BW _pdbx_nonpoly_scheme.auth_mon_id 4BW _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 6K3Y _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6K3Y _struct.title ;G-quadruplex complex with cyclic dinucleotide 3'-3' cGAMP ; _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 6K3Y _struct_keywords.text 'G-quadruplex, cGAMP, dinucleotide, vacancy, 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 6K3Y _struct_ref.pdbx_db_accession 6K3Y _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 6K3Y _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6K3Y _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _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 17 # _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)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 3850 ? # _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 ? # _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 3 N1 ? ? ? 1_555 A DG 6 O6 ? ? A DG 3 A DG 6 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 6 N7 ? ? A DG 3 A DG 6 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 3 N7 ? ? ? 1_555 A DG 14 N2 ? ? A DG 3 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DG 14 N1 ? ? A DG 3 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 7 O6 ? ? A DG 4 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 7 N7 ? ? A DG 4 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 4 N7 ? ? ? 1_555 A DG 15 N2 ? ? A DG 4 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DG 15 N1 ? ? A DG 4 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DG 10 O6 ? ? A DG 6 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DG 10 N7 ? ? A DG 6 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A DG 11 O6 ? ? A DG 7 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A DG 11 N7 ? ? A DG 7 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DG 12 O6 ? ? A DG 8 A DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DG 12 N7 ? ? A DG 8 A DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DG 14 O6 ? ? A DG 10 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DG 14 N7 ? ? A DG 10 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 11 N1 ? ? ? 1_555 A DG 15 O6 ? ? A DG 11 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 11 N2 ? ? ? 1_555 A DG 15 N7 ? ? A DG 11 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DG 12 N1 ? ? ? 1_555 A DG 16 O6 ? ? A DG 12 A DG 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A DG 12 N2 ? ? ? 1_555 A DG 16 N7 ? ? A DG 12 A DG 16 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 4BW _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'binding site for residue 4BW 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 5 DG A 4 ? DG A 4 . ? 1_555 ? 2 AC1 5 DT A 5 ? DT A 5 . ? 1_555 ? 3 AC1 5 DG A 8 ? DG A 8 . ? 1_555 ? 4 AC1 5 DG A 16 ? DG A 16 . ? 1_555 ? 5 AC1 5 DT A 17 ? DT A 17 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 7 _pdbx_validate_close_contact.auth_atom_id_1 "H1'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DT _pdbx_validate_close_contact.auth_seq_id_1 2 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 DG _pdbx_validate_close_contact.auth_seq_id_2 3 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.60 # _pdbx_nmr_ensemble.entry_id 6K3Y _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _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 6K3Y _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1 mM delta1, 1.5 mM cGAMP, 10 mM potassium chloride, 10 mM potassium phosphate, 100% D2O' '100% D2O' delta1-cGAMP-D2O solution ? 2 '1 mM delta1, 1.5 mM cGAMP, 10 mM potassium chloride, 10 mM potassium phosphate, 90% H2O/10% D2O' '90% H2O/10% D2O' delta1-cGAMP-H2O solution ? # 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 delta1 1 ? mM 'natural abundance' 1 cGAMP 1.5 ? mM 'natural abundance' 1 'potassium chloride' 10 ? mM 'natural abundance' 1 'potassium phosphate' 10 ? mM 'natural abundance' 2 delta1 1 ? mM 'natural abundance' 2 cGAMP 1.5 ? mM 'natural abundance' 2 'potassium chloride' 10 ? mM 'natural abundance' 2 'potassium phosphate' 10 ? mM 'natural abundance' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 298 atm 1 7 30 ? ? mM condition_1 ? pH ? ? K 2 283 atm 1 7 30 ? ? mM condition_2 ? pH ? ? 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 isotropic 2 1 2 '2D 1H-1H NOESY' 1 isotropic 6 2 2 '2D 1H-1H NOESY' 1 isotropic 3 1 1 '2D 1H-1H TOCSY' 1 isotropic 4 1 1 '2D 1H-13C HSQC aliphatic' 1 isotropic 5 1 1 '2D 1H-13C HSQC aromatic' 1 isotropic # _pdbx_nmr_refine.entry_id 6K3Y _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 7 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin ? 'Bruker Biospin' 2 processing TopSpin ? 'Bruker Biospin' 3 'peak picking' Sparky ? Goddard 4 'chemical shift assignment' Sparky ? Goddard 5 'data analysis' Sparky ? Goddard 6 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 7 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 4BW OAC O N N 1 4BW CBC C N N 2 4BW NAT N N N 3 4BW CBA C N N 4 4BW NAA N N N 5 4BW NAS N N N 6 4BW CBG C Y N 7 4BW CBE C Y N 8 4BW NAR N Y N 9 4BW CAL C Y N 10 4BW NBQ N Y N 11 4BW CBO C N R 12 4BW CBI C N R 13 4BW OAG O N N 14 4BW OAX O N N 15 4BW CBK C N R 16 4BW CAN C N N 17 4BW OAV O N N 18 4BW PBR P N N 19 4BW "O3'" O N N 20 4BW OAH O N N 21 4BW OAD O N N 22 4BW CBM C N S 23 4BW OAZ O N N 24 4BW PBS P N N 25 4BW OAI O N N 26 4BW OAE O N N 27 4BW "O5'" O N N 28 4BW "C5'" C N N 29 4BW "C4'" C N R 30 4BW "O4'" O N N 31 4BW "C3'" C N S 32 4BW "C2'" C N R 33 4BW "O2'" O N N 34 4BW "C1'" C N R 35 4BW N9 N Y N 36 4BW C8 C Y N 37 4BW N7 N Y N 38 4BW C5 C Y N 39 4BW C4 C Y N 40 4BW N3 N Y N 41 4BW C2 C Y N 42 4BW N1 N Y N 43 4BW C6 C Y N 44 4BW N6 N N N 45 4BW H1 H N N 46 4BW H2 H N N 47 4BW H3 H N N 48 4BW H4 H N N 49 4BW H5 H N N 50 4BW H6 H N N 51 4BW H7 H N N 52 4BW H8 H N N 53 4BW H9 H N N 54 4BW H10 H N N 55 4BW H11 H N N 56 4BW H12 H N N 57 4BW H13 H N N 58 4BW H14 H N N 59 4BW H15 H N N 60 4BW H16 H N N 61 4BW H17 H N N 62 4BW H18 H N N 63 4BW H19 H N N 64 4BW H20 H N N 65 4BW H21 H N N 66 4BW H22 H N N 67 4BW H23 H N N 68 4BW H24 H N N 69 DG OP3 O N N 70 DG P P N N 71 DG OP1 O N N 72 DG OP2 O N N 73 DG "O5'" O N N 74 DG "C5'" C N N 75 DG "C4'" C N R 76 DG "O4'" O N N 77 DG "C3'" C N S 78 DG "O3'" O N N 79 DG "C2'" C N N 80 DG "C1'" C N R 81 DG N9 N Y N 82 DG C8 C Y N 83 DG N7 N Y N 84 DG C5 C Y N 85 DG C6 C N N 86 DG O6 O N N 87 DG N1 N N N 88 DG C2 C N N 89 DG N2 N N N 90 DG N3 N N N 91 DG C4 C Y N 92 DG HOP3 H N N 93 DG HOP2 H N N 94 DG "H5'" H N N 95 DG "H5''" H N N 96 DG "H4'" H N N 97 DG "H3'" H N N 98 DG "HO3'" H N N 99 DG "H2'" H N N 100 DG "H2''" H N N 101 DG "H1'" H N N 102 DG H8 H N N 103 DG H1 H N N 104 DG H21 H N N 105 DG H22 H N N 106 DT OP3 O N N 107 DT P P N N 108 DT OP1 O N N 109 DT OP2 O N N 110 DT "O5'" O N N 111 DT "C5'" C N N 112 DT "C4'" C N R 113 DT "O4'" O N N 114 DT "C3'" C N S 115 DT "O3'" O N N 116 DT "C2'" C N N 117 DT "C1'" C N R 118 DT N1 N N N 119 DT C2 C N N 120 DT O2 O N N 121 DT N3 N N N 122 DT C4 C N N 123 DT O4 O N N 124 DT C5 C N N 125 DT C7 C N N 126 DT C6 C N N 127 DT HOP3 H N N 128 DT HOP2 H N N 129 DT "H5'" H N N 130 DT "H5''" H N N 131 DT "H4'" H N N 132 DT "H3'" H N N 133 DT "HO3'" H N N 134 DT "H2'" H N N 135 DT "H2''" H N N 136 DT "H1'" H N N 137 DT H3 H N N 138 DT H71 H N N 139 DT H72 H N N 140 DT H73 H N N 141 DT H6 H N N 142 # 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 4BW NAA CBA sing N N 1 4BW CBA NAS doub N N 2 4BW CBA NAT sing N N 3 4BW NAS CBG sing N N 4 4BW NAT CBC sing N N 5 4BW OAG CBI sing N N 6 4BW CBG NBQ sing Y N 7 4BW CBG CBE doub Y N 8 4BW CBC CBE sing N N 9 4BW CBC OAC doub N N 10 4BW OAI PBS doub N N 11 4BW CBI CBO sing N N 12 4BW CBI CBM sing N N 13 4BW CBO NBQ sing N N 14 4BW CBO OAX sing N N 15 4BW NBQ CAL sing Y N 16 4BW CBE NAR sing Y N 17 4BW OAE PBS sing N N 18 4BW OAX CBK sing N N 19 4BW PBS OAZ sing N N 20 4BW PBS "O5'" sing N N 21 4BW OAZ CBM sing N N 22 4BW CBM CBK sing N N 23 4BW CAL NAR doub Y N 24 4BW CBK CAN sing N N 25 4BW N6 C6 sing N N 26 4BW N7 C8 doub Y N 27 4BW N7 C5 sing Y N 28 4BW "O5'" "C5'" sing N N 29 4BW C8 N9 sing Y N 30 4BW C6 C5 doub Y N 31 4BW C6 N1 sing Y N 32 4BW C5 C4 sing Y N 33 4BW CAN OAV sing N N 34 4BW "C5'" "C4'" sing N N 35 4BW OAV PBR sing N N 36 4BW N9 C4 sing Y N 37 4BW N9 "C1'" sing N N 38 4BW N1 C2 doub Y N 39 4BW C4 N3 doub Y N 40 4BW "O4'" "C4'" sing N N 41 4BW "O4'" "C1'" sing N N 42 4BW "C4'" "C3'" sing N N 43 4BW "C3'" "C2'" sing N N 44 4BW "C3'" "O3'" sing N N 45 4BW "C1'" "C2'" sing N N 46 4BW C2 N3 sing Y N 47 4BW PBR OAD doub N N 48 4BW PBR "O3'" sing N N 49 4BW PBR OAH sing N N 50 4BW "C2'" "O2'" sing N N 51 4BW NAT H1 sing N N 52 4BW NAA H2 sing N N 53 4BW NAA H3 sing N N 54 4BW CAL H4 sing N N 55 4BW CBO H5 sing N N 56 4BW CBI H6 sing N N 57 4BW OAG H7 sing N N 58 4BW CBK H8 sing N N 59 4BW CAN H9 sing N N 60 4BW CAN H10 sing N N 61 4BW OAH H11 sing N N 62 4BW CBM H12 sing N N 63 4BW OAE H13 sing N N 64 4BW "C5'" H14 sing N N 65 4BW "C5'" H15 sing N N 66 4BW "C4'" H16 sing N N 67 4BW "C3'" H17 sing N N 68 4BW "C2'" H18 sing N N 69 4BW "O2'" H19 sing N N 70 4BW "C1'" H20 sing N N 71 4BW C8 H21 sing N N 72 4BW C2 H22 sing N N 73 4BW N6 H23 sing N N 74 4BW N6 H24 sing N N 75 DG OP3 P sing N N 76 DG OP3 HOP3 sing N N 77 DG P OP1 doub N N 78 DG P OP2 sing N N 79 DG P "O5'" sing N N 80 DG OP2 HOP2 sing N N 81 DG "O5'" "C5'" sing N N 82 DG "C5'" "C4'" sing N N 83 DG "C5'" "H5'" sing N N 84 DG "C5'" "H5''" sing N N 85 DG "C4'" "O4'" sing N N 86 DG "C4'" "C3'" sing N N 87 DG "C4'" "H4'" sing N N 88 DG "O4'" "C1'" sing N N 89 DG "C3'" "O3'" sing N N 90 DG "C3'" "C2'" sing N N 91 DG "C3'" "H3'" sing N N 92 DG "O3'" "HO3'" sing N N 93 DG "C2'" "C1'" sing N N 94 DG "C2'" "H2'" sing N N 95 DG "C2'" "H2''" sing N N 96 DG "C1'" N9 sing N N 97 DG "C1'" "H1'" sing N N 98 DG N9 C8 sing Y N 99 DG N9 C4 sing Y N 100 DG C8 N7 doub Y N 101 DG C8 H8 sing N N 102 DG N7 C5 sing Y N 103 DG C5 C6 sing N N 104 DG C5 C4 doub Y N 105 DG C6 O6 doub N N 106 DG C6 N1 sing N N 107 DG N1 C2 sing N N 108 DG N1 H1 sing N N 109 DG C2 N2 sing N N 110 DG C2 N3 doub N N 111 DG N2 H21 sing N N 112 DG N2 H22 sing N N 113 DG N3 C4 sing N N 114 DT OP3 P sing N N 115 DT OP3 HOP3 sing N N 116 DT P OP1 doub N N 117 DT P OP2 sing N N 118 DT P "O5'" sing N N 119 DT OP2 HOP2 sing N N 120 DT "O5'" "C5'" sing N N 121 DT "C5'" "C4'" sing N N 122 DT "C5'" "H5'" sing N N 123 DT "C5'" "H5''" sing N N 124 DT "C4'" "O4'" sing N N 125 DT "C4'" "C3'" sing N N 126 DT "C4'" "H4'" sing N N 127 DT "O4'" "C1'" sing N N 128 DT "C3'" "O3'" sing N N 129 DT "C3'" "C2'" sing N N 130 DT "C3'" "H3'" sing N N 131 DT "O3'" "HO3'" sing N N 132 DT "C2'" "C1'" sing N N 133 DT "C2'" "H2'" sing N N 134 DT "C2'" "H2''" sing N N 135 DT "C1'" N1 sing N N 136 DT "C1'" "H1'" sing N N 137 DT N1 C2 sing N N 138 DT N1 C6 sing N N 139 DT C2 O2 doub N N 140 DT C2 N3 sing N N 141 DT N3 C4 sing N N 142 DT N3 H3 sing N N 143 DT C4 O4 doub N N 144 DT C4 C5 sing N N 145 DT C5 C7 sing N N 146 DT C5 C6 doub N N 147 DT C7 H71 sing N N 148 DT C7 H72 sing N N 149 DT C7 H73 sing N N 150 DT C6 H6 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6K3Y 'double helix' 6K3Y '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 3 1_555 A DG 14 1_555 -1.435 -3.864 0.141 0.807 2.603 86.811 1 A_DG3:DG14_A A 3 ? A 14 ? 6 3 1 A DG 4 1_555 A DG 15 1_555 -0.422 -3.567 0.405 -2.344 -3.066 96.959 2 A_DG4:DG15_A A 4 ? A 15 ? 6 3 1 A DG 12 1_555 A DG 16 1_555 1.482 3.793 -0.100 0.985 -0.196 -85.914 3 A_DG12:DG16_A A 12 ? A 16 ? 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 3 1_555 A DG 14 1_555 A DG 4 1_555 A DG 15 1_555 -0.379 -0.295 3.309 1.027 -2.102 31.286 -0.145 0.896 3.307 -3.891 -1.901 31.371 1 AA_DG3DG4:DG15DG14_AA A 3 ? A 14 ? A 4 ? A 15 ? 1 A DG 4 1_555 A DG 15 1_555 A DG 12 1_555 A DG 16 1_555 0.003 1.305 3.620 -3.638 2.167 -63.375 -1.345 -0.172 3.573 -2.060 -3.459 -63.502 2 AA_DG4DG12:DG16DG15_AA A 4 ? A 15 ? A 12 ? A 16 ? # _pdbx_audit_support.funding_organization 'National Research Foundation (Singapore)' _pdbx_audit_support.country Singapore _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE II' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 6K3Y _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_