Header list of 1y8d.pdb file
Complete list - 2 20 Bytes
HEADER DNA 11-DEC-04 1Y8D
TITLE DIMERIC PARALLEL-STRANDED TETRAPLEX WITH 3+1 5' G-TETRAD INTERFACE,
TITLE 2 SINGLE-RESIDUE CHAIN REVERSAL LOOPS AND GAG TRIAD IN THE CONTEXT OF
TITLE 3 A(GGGG) PENTAD
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: HIV INTEGRASE INHIBITOR SEQUENCE;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: DNA APTAMER OBTAINED BY SELEX OF ODN INHIBITING RNASE
SOURCE 4 H ACTIVITY OF HIV REVERSE TRANSCRIPTASE
KEYWDS DIMERIC PARALLEL-STRANDED QUADRUPLEX; DNA APTAMER;HIV-1 INTEGRASE
KEYWDS 2 INHIBITOR DESIGN; 3+1 G-TETRAD; SINGLE NUCLEOTIDE CHAIN REVERSAL
KEYWDS 3 LOOP; GAG TRIAD; (A)GGGG PENTAD, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.T.PHAN,V.V.KURYAVYI,J.-B.MA,A.FAURE,M.-L.ANDREOLA,D.J.PATEL
REVDAT 3 02-MAR-22 1Y8D 1 REMARK
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,M.-L.ANDREOLA,
JRNL AUTH 2 D.J.PATEL
JRNL TITL AN INTERLOCKED DIMERIC PARALLEL-STRANDED DNA QUADRUPLEX: A
JRNL TITL 2 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 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 2000, X-PLOR 3.851
REMARK 3 AUTHORS : ACCELRYS (FELIX), A.T.BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 1689 RESTRAINTS, 283 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 3
REMARK 3 NEGATIVE RESTRAINTS, 84 DIHEDRAL ANGLE RESTRAINTS,104 DISTANCE
REMARK 3 RESTRAINTS FROM HYDROGEN BONDS, 243 INTENSITY RESTRAINTS (EACH
REMARK 3 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 DEPOSITION ID IS D_1000031244.
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 : 1 ATM
REMARK 210 SAMPLE CONTENTS : DNA 15N,13C; DNA 15N,13C
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 1H-31P COSY;
REMARK 210 1H-15N JRHMQC; 1H-13C 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 : 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, 1H
REMARK 210 -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 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 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. = 4.0 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. = 2.5 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. = 2.5 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. = 2.0 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 A(GGGG)A
REMARK 900 DNA HEXAD
REMARK 900 RELATED ID: 1JJP RELATED DB: PDB
REMARK 900 A TETRAPLEX CONTAINING A GAG TRIAD IN THE CONTEXT OF AN A(GGGG) DNA
REMARK 900 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
MODEL 1
Complete list - 2 20 Bytes