10 20 30 40 50 60 70 80 1K8L - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 24-OCT-01 1K8L
TITLE XBY6: AN ANALOG OF CK14 CONTAINING 6 DITHIOPHOSPHATE GROUPS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIRST STRAND OF CK14 DNA DUPLEX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DITHIOATED AT T10, C11; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE COMPND 8 CK1; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SECOND STRAND OF CK14 DNA DUPLEX; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: DITHIOATED AT G17, C22, C24, G27; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE COMPND 16 CK1
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED WITH BOTH NORMAL SOURCE 4 PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE SOURCE 5 CHEMISTRY; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: SYNTHESIZED WITH BOTH NORMAL SOURCE 9 PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE SOURCE 10 CHEMISTRY
KEYWDS XBY6, CK14, CK1, PHOSPHORODITHIOATE, NF-KB, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT, AUTHOR 2 S.VENKITACHALAM,N.HERZOG,B.A.LUXON,D.G.GORENSTEIN
REVDAT 2 24-FEB-09 1K8L 1 VERSN REVDAT 1 15-APR-03 1K8L 0
JRNL AUTH D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT, JRNL AUTH 2 S.VENKITACHALAM,N.HERZOG,B.A.LUXON,D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE AND DESIGN OF DITHIOPHOSPHATE JRNL TITL 2 BACKBONE APTAMERS TARGETING TRANSCRIPTION FACTOR JRNL TITL 3 NF-KAPPAB JRNL REF BIOORG.CHEM. V. 30 396 2002 JRNL REFN ISSN 0045-2068 JRNL PMID 12642125 JRNL DOI 10.1016/S0045-2068(02)00510-2
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5 REMARK 3 AUTHORS : CASE,KOLLMAN, ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE RESTRAINTS WERE DERIVED BY REMARK 3 MORASS 2.5 USING A TOTAL RELAXATION MATRIX APPROACH. AMBER 5 REMARK 3 WAS USED FOR MD AND MINIMIZATION. THE DEPOSITED STRUCTURE REMARK 3 REPRESENTS THE AVERAGE OF TEN FINAL STRUCTURES
REMARK 4 REMARK 4 1K8L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-01. REMARK 100 THE RCSB ID CODE IS RCSB014695.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : 100 MM; 100 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX, 12 MM NA2HPO4, 8 REMARK 210 MM NAH2PO4, 56 MM NACL, 50 UM REMARK 210 NAN3; 1 MM DUPLEX, 12 MM REMARK 210 NA2HPO4, 8 MM NAH2PO4, 56MM REMARK 210 NACL, 50 UM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.5, AMBER 5 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. PROTON RESONANCES WERE ASSIGNED USING REMARK 210 COSY, TOCSY, AND NOESY DATA
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 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 DC A 1 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A 1 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 23 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 23 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG B 28 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K8J RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CK14, THE NON-THIOATED ANALOG OF XBY6 REMARK 900 RELATED ID: 1K8N RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CK14, AN ANALOG WITH 2 PHOSPHORODITHIOATES
DBREF 1K8L A 1 14 PDB 1K8L 1K8L 1 14 DBREF 1K8L B 15 28 PDB 1K8L 1K8L 15 28
SEQRES 1 A 14 DC DC DA DG DG DA DG DA DT T2S C2S DC DA SEQRES 2 A 14 DC SEQRES 1 B 14 DG DT G2S DG DA DA DT C2S DT C2S DC DT G2S SEQRES 2 B 14 DG
MODRES 1K8L T2S A 10 T THYMIDINE-5'-DITHIOPHOSPHORATE MODRES 1K8L C2S A 11 DC CYTIDINE-5'-DITHIOPHOSPHORATE MODRES 1K8L G2S B 17 DG GUANOSINE-5'-DITHIOPHOSPHORATE MODRES 1K8L C2S B 22 DC CYTIDINE-5'-DITHIOPHOSPHORATE MODRES 1K8L C2S B 24 DC CYTIDINE-5'-DITHIOPHOSPHORATE MODRES 1K8L G2S B 27 DG GUANOSINE-5'-DITHIOPHOSPHORATE
HET T2S A 10 32 HET C2S A 11 30 HET G2S B 17 33 HET C2S B 22 30 HET C2S B 24 30 HET G2S B 27 33
HETNAM T2S THYMIDINE-5'-DITHIOPHOSPHORATE HETNAM C2S CYTIDINE-5'-DITHIOPHOSPHORATE HETNAM G2S GUANOSINE-5'-DITHIOPHOSPHORATE
FORMUL 1 T2S C10 H15 N2 O6 P S2 FORMUL 1 C2S 3(C9 H14 N3 O5 P S2) FORMUL 2 G2S 2(C10 H14 N5 O5 P S2)
LINK O3' DT A 9 P T2S A 10 1555 1555 1.62 LINK O3' T2S A 10 P C2S A 11 1555 1555 1.62 LINK O3' C2S A 11 P DC A 12 1555 1555 1.62 LINK O3' DT B 16 P G2S B 17 1555 1555 1.62 LINK O3' G2S B 17 P DG B 18 1555 1555 1.62 LINK O3' DT B 21 P C2S B 22 1555 1555 1.62 LINK O3' C2S B 22 P DT B 23 1555 1555 1.62 LINK O3' DT B 23 P C2S B 24 1555 1555 1.62 LINK O3' C2S B 24 P DC B 25 1555 1555 1.62 LINK O3' DT B 26 P G2S B 27 1555 1555 1.62 LINK O3' G2S B 27 P DG B 28 1555 1555 1.61
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