HEADER HIV-1 10-DEC-03 1UTS TITLE DESIGNED HIV-1 TAR BINDING LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP COMPND 3 *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3'); COMPND 4 CHAIN: B; COMPND 5 SYNONYM: HIV-1 TAR RNA; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CONTAINS TAR BULGE (BINDING SITE FOR HIV-1 TAT) AND COMPND 8 STEM-LOOP (BINDING SITE FOR CYCLIN/CDK9 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11676; SOURCE 6 OTHER_DETAILS: 29 NUCLEOTIDE SEQUENCE COMPRISING PRIMARY BINDING SOURCE 7 SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA POLYMERASE OFF OF A DNA SOURCE 8 TEMPLATE KEYWDS HIV-1, TAR RNA, DRUG DESIGN, ANTIVIRAL, LIGAND BINDING, KEYWDS 2 CONFORMATIONAL CHANGE EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR B.DAVIS,A.I.H.MURCHIE,F.ABOUL-ELA,J.KARN REVDAT 3 05-MAY-21 1UTS 1 JRNL REMARK REVDAT 2 24-FEB-09 1UTS 1 VERSN REVDAT 1 12-FEB-04 1UTS 0 JRNL AUTH A.I.MURCHIE,B.DAVIS,C.ISEL,M.AFSHAR,M.J.DRYSDALE,J.BOWER, JRNL AUTH 2 A.J.POTTER,I.D.STARKEY,T.M.SWARBRICK,S.MIRZA,C.D.PRESCOTT, JRNL AUTH 3 P.VAGLIO,F.ABOUL-ELA,J.KARN JRNL TITL STRUCTURE-BASED DRUG DESIGN TARGETING AN INACTIVE RNA JRNL TITL 2 CONFORMATION: EXPLOITING THE FLEXIBILITY OF HIV-1 TAR RNA. JRNL REF J.MOL.BIOL. V. 336 625 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15095977 JRNL DOI 10.1016/J.JMB.2003.12.028 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS WERE ACCORDING TO REMARK 3 STANDARD METHODS (SEE JOURNAL CITATION ABOVE AND G. VARANI, F. REMARK 3 ABOUL-ELA, AND F. ALLAIN, NMR INVESTIGATION OF RNA STRUCTURE. REMARK 3 FROM PROGRESS IN NMR SPECTROSCOPY, V. 29, P. 51-127. REMARK 4 REMARK 4 1UTS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1290014110. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; HCCH-TOCSY; HCCH-COSY; REMARK 210 NOESY-HSQC; LONG RANGE 15N-1H REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : NOE-RESTRAINED DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED TAR RNA IN D2O AT 303 K, AND REMARK 210 UNLABELED TAR RNA IN H2O AT 278 K, ALL COMPLEXED WITH THE REMARK 210 SYNTHETIC LIGAND, RBT550 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G B 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G B 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G B 18 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A B 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G B 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 21 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A B 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G B 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A B 27 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G B 28 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G B 32 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 32 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G B 33 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 33 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A B 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G B 36 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G B 36 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G B 43 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 43 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G B 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G B 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G B 18 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A B 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G B 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G B 21 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A B 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G B 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G B 26 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G B 28 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G B 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G B 32 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G B 32 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G B 33 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G B 33 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A B 35 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G B 36 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G B 36 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G B 43 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G B 43 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G B 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 384 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P13 B1046 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UUI RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND REMARK 900 RELATED ID: 1UUD RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND DBREF 1UTS B 17 45 PDB 1UTS 1UTS 17 45 SEQRES 1 B 29 G G C A G A U C U G A G C SEQRES 2 B 29 C U G G G A G C U C U C U SEQRES 3 B 29 G C C HET P13 B1046 67 HETNAM P13 N-[2-(3-AMINOPROPOXY)-5-(1H-INDOL-5-YL)BENZYL]-N-(2- HETNAM 2 P13 PIPERAZIN-1-YLETHYL)AMINE HETSYN P13 RBT550 INHIBITOR FORMUL 2 P13 C24 H33 N5 O SITE 1 AC1 5 A B 22 U B 23 G B 26 C B 39 SITE 2 AC1 5 U B 40 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