HEADER DNA 11-DEC-04 1Y8D TITLE DIMERIC PARALLEL-STRANDED TETRAPLEX WITH 3+1 5' G-TETRAD TITLE 2 INTERFACE, SINGLE-RESIDUE CHAIN REVERSAL LOOPS AND GAG TITLE 3 TRIAD IN THE CONTEXT OF A(GGGG) PENTAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3'; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: HIV INTEGRASE INHIBITOR SEQUENCE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA APTAMER OBTAINED BY SELEX OF ODN SOURCE 4 INHIBITING RNASE H ACTIVITY OF HIV REVERSE TRANSCRIPTASE KEYWDS DIMERIC PARALLEL-STRANDED QUADRUPLEX; DNA APTAMER;HIV-1 KEYWDS 2 INTEGRASE INHIBITOR DESIGN; 3+1 G-TETRAD; SINGLE NUCLEOTIDE KEYWDS 3 CHAIN REVERSAL LOOP; GAG TRIAD; (A)GGGG PENTAD EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.T.PHAN,V.V.KURYAVYI,J.-B.MA,A.FAURE,M.-L.ANDREOLA, AUTHOR 2 D.J.PATEL REVDAT 2 24-FEB-09 1Y8D 1 VERSN REVDAT 1 01-FEB-05 1Y8D 0 JRNL AUTH A.T.PHAN,V.V.KURYAVYI,J.-B.MA,A.FAURE, JRNL AUTH 2 M.-L.ANDREOLA,D.J.PATEL JRNL TITL AN INTERLOCKED DIMERIC PARALLEL-STRANDED DNA JRNL TITL 2 QUADRUPLEX: A POTENT INHIBITOR OF HIV-1 INTEGRASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 634 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15637158 JRNL DOI 10.1073/PNAS.0406278102 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : A.T.BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 1689 RESTRAINTS, 283 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 3 NEGATIVE RESTRAINTS, 84 DIHEDRAL ANGLE RESTRAINTS,104 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS, 243 INTENSITY REMARK 3 RESTRAINTS (EACH OF FIVE MIXING TIMES) REMARK 4 REMARK 4 1Y8D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031244. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 90 MM KCL REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : DNA 15N,13C; DNA 15N,13C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 1H-31P REMARK 210 COSY, 1H-15N JRHMQC, 1H-13C REMARK 210 JRHMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, VNMR 6.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY; SIMULATED REMARK 210 ANNEALING; MOLECULAR DYNAMICS; REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED,BACK CALCULATED DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE EXPERIMENTS 1H-15N HMBC, 1H-13C HMBC, 1H-13C HSQC, REMARK 210 1H-13C SHMBC WERE PERFORMED FOR ASSIGNMENTS 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DG A 1 C5' DG A 1 C4' 0.050 REMARK 500 1 DG B 1 C5' DG B 1 C4' 0.051 REMARK 500 2 DG A 1 C5' DG A 1 C4' 0.049 REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.043 REMARK 500 2 DG B 1 C5' DG B 1 C4' 0.048 REMARK 500 3 DG A 1 C5' DG A 1 C4' 0.045 REMARK 500 3 DG A 10 C5' DG A 10 C4' 0.048 REMARK 500 3 DG B 1 C5' DG B 1 C4' 0.046 REMARK 500 3 DG B 10 C5' DG B 10 C4' 0.050 REMARK 500 4 DG A 1 C5' DG A 1 C4' 0.051 REMARK 500 4 DG A 10 C5' DG A 10 C4' 0.042 REMARK 500 4 DG B 1 C5' DG B 1 C4' 0.051 REMARK 500 4 DG B 15 C5' DG B 15 C4' 0.042 REMARK 500 5 DG A 1 C5' DG A 1 C4' 0.046 REMARK 500 5 DG A 10 C5' DG A 10 C4' 0.049 REMARK 500 5 DG B 1 C5' DG B 1 C4' 0.046 REMARK 500 5 DG B 10 C5' DG B 10 C4' 0.049 REMARK 500 6 DG A 1 C5' DG A 1 C4' 0.049 REMARK 500 6 DG B 1 C5' DG B 1 C4' 0.050 REMARK 500 7 DG A 1 C5' DG A 1 C4' 0.051 REMARK 500 7 DG B 1 C5' DG B 1 C4' 0.050 REMARK 500 8 DG A 1 C5' DG A 1 C4' 0.048 REMARK 500 8 DG B 1 C5' DG B 1 C4' 0.048 REMARK 500 9 DG A 1 C5' DG A 1 C4' 0.045 REMARK 500 9 DG A 10 C5' DG A 10 C4' 0.052 REMARK 500 9 DG B 1 C5' DG B 1 C4' 0.046 REMARK 500 9 DG B 10 C5' DG B 10 C4' 0.050 REMARK 500 10 DG A 1 C5' DG A 1 C4' 0.050 REMARK 500 10 DG A 2 C5' DG A 2 C4' 0.043 REMARK 500 10 DG B 1 C5' DG B 1 C4' 0.050 REMARK 500 10 DG B 2 C5' DG B 2 C4' 0.042 REMARK 500 10 DG B 15 C5' DG B 15 C4' 0.044 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG B 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG B 6 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DA B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 138 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EEG RELATED DB: PDB REMARK 900 A TETRAPLEX CONTAINING A GAG TRIAD IN THE CONTEXT OF AN REMARK 900 A(GGGG)A DNA HEXAD REMARK 900 RELATED ID: 1JJP RELATED DB: PDB REMARK 900 A TETRAPLEX CONTAINING A GAG TRIAD IN THE CONTEXT OF AN REMARK 900 A(GGGG) DNA PENTAD DBREF 1Y8D A 1 16 PDB 1Y8D 1Y8D 1 16 DBREF 1Y8D B 1 16 PDB 1Y8D 1Y8D 1 16 SEQRES 1 A 16 DG DG DG DG DT DG DG DG DA DG DG DA DG SEQRES 2 A 16 DG DG DT SEQRES 1 B 16 DG DG DG DG DT DG DG DG DA DG DG DA DG SEQRES 2 B 16 DG DG DT 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 188 0 0 0 0 0 0 6 0 0 0 4 END