HEADER ANTISENSE 29-DEC-00 1HHX TITLE SOLUTION STRUCTURE OF LNA3:RNA HYBRID CAVEAT 1HHX NUCLEIC ACID RESIDUES HAVE CHIRALITY ERRORS RESIDUE C A 1 AT CAVEAT 2 1HHX ATOM C5* RESIDUE C A 1 AT ATOM C5* COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5- D(*CP*+TP*GP*AP*+TP*AP*+TP*GP*C) -3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS ANTISENSE, LOCKED NUCLEIC ACID, LNA, RNA, HYBRID, RNASE H EXPDTA SOLUTION NMR NUMMDL 34 AUTHOR M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN REVDAT 4 15-MAY-24 1HHX 1 REMARK LINK REVDAT 3 24-FEB-09 1HHX 1 VERSN REVDAT 2 13-JUN-02 1HHX 1 CAVEAT REMARK MODRES ATOM REVDAT 2 2 1 TER HETATM CONECT REVDAT 1 30-MAY-02 1HHX 0 JRNL AUTH M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN JRNL TITL LOCKED NUCLEIC ACID (LNA) RECOGNITION OF RNA: NMR SOLUTION JRNL TITL 2 STRUCTURES OF LNA:RNA HYBRIDS JRNL REF J.AM.CHEM.SOC. V. 124 5974 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12022830 JRNL DOI 10.1021/JA012288D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.BONDENSGAARD,M.PETERSEN,S.K.SINGH,V.K.RAJWANSHI,R.KUMAR, REMARK 1 AUTH 2 J.WENGEL,J.P.JACOBSEN REMARK 1 TITL STRUCTURAL STUDIES OF LNA:RNA DUPLEXES BY NMR: CONFORMATIONS REMARK 1 TITL 2 AND IMPLICATIONS FOR RNASE H ACTIVITY. REMARK 1 REF CHEMISTRY V. 6 2687 2000 REMARK 1 REFN ISSN 0947-6539 REMARK 1 PMID 10985717 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DA, KOLLMAN, PA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 423 NOE DISTANCE RESTRAINTS REMARK 3 WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE REMARK 3 PROGRAM RANDMARDI. A FURTHER 58 NOE DISTANCE RESTRAINTS WERE REMARK 3 OBTAINED FROM NOESY IN H2O USING ISPA. 22 WATSON-CRICK BASE REMARK 3 PAIRING RESTRAINTS. REMARK 4 REMARK 4 1HHX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1290005713. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7E-3M LNA1:RNA, 0.1M NACL, 5E REMARK 210 -5M EDTA AND 1E-2M PHOSPHATE REMARK 210 BUFFER IN 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, AMBER, FELIX REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 34 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 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 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 DC A 1 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 3 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 6 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G B 10 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 C B 11 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A B 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U B 13 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 U B 15 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 A B 17 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 1 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DC A 1 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 2 DC A 1 C3' - C2' - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DA A 6 O4' - C1' - C2' ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 8 C4' - C3' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G B 10 C4' - C3' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 2 C B 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 A B 12 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U B 13 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 U B 15 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 A B 17 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 DC A 1 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DA A 6 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DG A 8 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG A 8 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G B 10 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 632 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DG A 3 0.10 SIDE CHAIN REMARK 500 1 DC A 9 0.06 SIDE CHAIN REMARK 500 1 G B 10 0.09 SIDE CHAIN REMARK 500 1 A B 12 0.07 SIDE CHAIN REMARK 500 1 A B 14 0.07 SIDE CHAIN REMARK 500 1 A B 17 0.07 SIDE CHAIN REMARK 500 1 G B 18 0.08 SIDE CHAIN REMARK 500 2 DG A 3 0.08 SIDE CHAIN REMARK 500 2 DC A 9 0.07 SIDE CHAIN REMARK 500 2 G B 10 0.09 SIDE CHAIN REMARK 500 2 C B 11 0.06 SIDE CHAIN REMARK 500 2 A B 12 0.07 SIDE CHAIN REMARK 500 2 A B 17 0.06 SIDE CHAIN REMARK 500 2 G B 18 0.09 SIDE CHAIN REMARK 500 3 DG A 3 0.09 SIDE CHAIN REMARK 500 3 G B 10 0.08 SIDE CHAIN REMARK 500 3 A B 12 0.07 SIDE CHAIN REMARK 500 3 A B 17 0.07 SIDE CHAIN REMARK 500 3 G B 18 0.10 SIDE CHAIN REMARK 500 4 DG A 3 0.08 SIDE CHAIN REMARK 500 4 DC A 9 0.06 SIDE CHAIN REMARK 500 4 G B 10 0.09 SIDE CHAIN REMARK 500 4 A B 14 0.06 SIDE CHAIN REMARK 500 4 A B 17 0.06 SIDE CHAIN REMARK 500 4 G B 18 0.11 SIDE CHAIN REMARK 500 5 DG A 3 0.10 SIDE CHAIN REMARK 500 5 DC A 9 0.06 SIDE CHAIN REMARK 500 5 G B 10 0.08 SIDE CHAIN REMARK 500 5 A B 12 0.07 SIDE CHAIN REMARK 500 5 A B 17 0.09 SIDE CHAIN REMARK 500 5 G B 18 0.07 SIDE CHAIN REMARK 500 6 DG A 3 0.10 SIDE CHAIN REMARK 500 6 DC A 9 0.06 SIDE CHAIN REMARK 500 6 G B 10 0.09 SIDE CHAIN REMARK 500 6 A B 12 0.07 SIDE CHAIN REMARK 500 6 A B 17 0.07 SIDE CHAIN REMARK 500 6 G B 18 0.09 SIDE CHAIN REMARK 500 7 DG A 3 0.09 SIDE CHAIN REMARK 500 7 DG A 8 0.07 SIDE CHAIN REMARK 500 7 DC A 9 0.07 SIDE CHAIN REMARK 500 7 G B 10 0.09 SIDE CHAIN REMARK 500 7 A B 14 0.05 SIDE CHAIN REMARK 500 7 A B 17 0.06 SIDE CHAIN REMARK 500 7 G B 18 0.10 SIDE CHAIN REMARK 500 8 DG A 3 0.09 SIDE CHAIN REMARK 500 8 DC A 9 0.06 SIDE CHAIN REMARK 500 8 G B 10 0.09 SIDE CHAIN REMARK 500 8 A B 17 0.08 SIDE CHAIN REMARK 500 8 G B 18 0.09 SIDE CHAIN REMARK 500 9 DG A 3 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 216 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HG9 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DNA:RNA HYBRID REMARK 900 RELATED ID: 1HHW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LNA1:RNA HYBRID REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN A RESIDUES 2,5,7 ARE LOCKED NUCLEIC ACIDS OR REMARK 999 (1R,3R,4R,7S)-7-HYDROXY-1-HYDROXYMETHYL-3-(THYMIN-1-YL)- REMARK 999 2,5-DIOXABICYCLO[2.2.1]HEPTANE DBREF 1HHX A 1 9 PDB 1HHX 1HHX 1 9 DBREF 1HHX B 10 18 PDB 1HHX 1HHX 10 18 SEQRES 1 A 9 DC TLN DG DA TLN DA TLN DG DC SEQRES 1 B 9 G C A U A U C A G MODRES 1HHX TLN A 2 DU MODRES 1HHX TLN A 5 DU MODRES 1HHX TLN A 7 DU HET TLN A 2 34 HET TLN A 5 34 HET TLN A 7 34 HETNAM TLN [(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5- HETNAM 2 TLN DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 TLN PHOSPHATE FORMUL 1 TLN 3(C11 H15 N2 O9 P) LINK O3' DC A 1 P TLN A 2 1555 1555 1.61 LINK O3' TLN A 2 P DG A 3 1555 1555 1.61 LINK O3' DA A 4 P TLN A 5 1555 1555 1.63 LINK O3' TLN A 5 P DA A 6 1555 1555 1.61 LINK O3' DA A 6 P TLN A 7 1555 1555 1.62 LINK O3' TLN A 7 P DG A 8 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 MODEL 1