HEADER DNA 19-AUG-22 7YVW TITLE NMR DETERMINATION OF THE 2:1 BINDING MOTIF STRUCTURE INVOLVING TITLE 2 CYTOSINE FLIPPING OUT FOR THE RECOGNITION OF THE CGG/CGG TRIAD DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS GG MISMATCH, DRUG, COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR K.FURUITA,T.YAMADA,S.SAKURABAYASHI,M.NOMURA,C.KOJIMA,K.NAKATANI REVDAT 2 15-MAY-24 7YVW 1 REMARK REVDAT 1 14-JUN-23 7YVW 0 JRNL AUTH T.YAMADA,K.FURUITA,S.SAKURABAYASHI,M.NOMURA,C.KOJIMA, JRNL AUTH 2 K.NAKATANI JRNL TITL NMR DETERMINATION OF THE 2:1 BINDING COMPLEX OF JRNL TITL 2 NAPHTHYRIDINE CARBAMATE DIMER (NCD) AND CGG/CGG TRIAD IN JRNL TITL 3 DOUBLE-STRANDED DNA. JRNL REF NUCLEIC ACIDS RES. V. 50 9621 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36095126 JRNL DOI 10.1093/NAR/GKAC740 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031584. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.5 MM NCD-GG1, 20 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY (200 MS); 2D 1H-13C REMARK 210 HSQC; 2D 1H-31P HSQC; 2D DQF- REMARK 210 COSY; 2D TOCSY; 2D NOESY (30 MS) REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRFAM-SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36507 RELATED DB: BMRB REMARK 900 NMR DETERMINATION OF THE 2:1 BINDING MOTIF STRUCTURE INVOLVING REMARK 900 CYTOSINE FLIPPING OUT FOR THE RECOGNITION OF THE CGG/CGG TRIAD DNA DBREF 7YVW A 1 11 PDB 7YVW 7YVW 1 11 DBREF 7YVW B 12 22 PDB 7YVW 7YVW 12 22 SEQRES 1 A 11 DC DT DA DA DC DG DG DA DA DT DG SEQRES 1 B 11 DC DA DT DT DC DG DG DT DT DA DG HET B2R A 101 66 HET B2R A 102 66 HETNAM B2R 3-[3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL) HETNAM 2 B2R CARBAMOYLOXY]PROPYLAMINO]PROPYL ~{N}-(7-METHYL-1,8- HETNAM 3 B2R NAPHTHYRIDIN-2-YL)CARBAMATE HETSYN B2R NAPHTHYRIDINE CARBAMATE DIMER FORMUL 3 B2R 2(C26 H29 N7 O4) CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1