HEADER HIV-1 18-DEC-03 1UUD TITLE NMR STRUCTURE OF A SYNTHETIC SMALL MOLECULE, RBT203, BOUND TO HIV-1 TITLE 2 TAR RNA 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: BULGED STEM LOOP REGION FROM 5'LTR OF HIV-1 MRNA- COMPND 8 BINDING SITE FOR TRANSCRIPTIONAL ACTIVATOR PROTEIN TAT. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1 (CLONE 12); SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11706; 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, LIGAND-RNA INTERACTION, RNA BULGE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR B.DAVIS,M.AFSHAR,G.VARANI,J.KARN,A.I.H.MURCHIE,G.LENTZEN, AUTHOR 2 M.J.DRYSDALE,A.J.POTTER,J.BOWER,F.ABOUL-ELA REVDAT 3 15-MAY-24 1UUD 1 REMARK REVDAT 2 24-FEB-09 1UUD 1 VERSN REVDAT 1 15-MAR-04 1UUD 0 JRNL AUTH B.DAVIS,M.AFSHAR,G.VARANI,A.I.H.MURCHIE,J.KARN,G.LENTZEN, JRNL AUTH 2 M.J.DRYSDALE,J.BOWER,A.J.POTTER,F.ABOUL-ELA JRNL TITL RATIONAL DESIGN OF INHIBITORS OF HIV-1 TAR RNA THROUGH THE JRNL TITL 2 STABILISATION OF ELECTROSTATIC "HOT SPOTS" JRNL REF J.MOL.BIOL. V. 336 343 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 14757049 JRNL DOI 10.1016/J.JMB.2003.12.046 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.ABOUL-ELA,J.JKARN,G.VARANI REMARK 1 TITL THE STRUCTURE OF THE HUMAN IMMUNODEFICIENCY VIRUS REMARK 1 TITL 2 RECOGNITION BY TAT PROTEIN REMARK 1 REF J.MOL.BIOL. V. 253 313 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7563092 REMARK 1 DOI 10.1006/JMBI.1995.0555 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 INCLUDED A NUMBER OF REMARK 3 MODELLING CONSTRAINTS BASED UPON PREVIOUSLY PUBLISHED DATA, AS REMARK 3 WELL AS FINAL GENTLE REFINEMENT STEP USING CHARMM. DETAILS CAN REMARK 3 BE FOUND IN THE JOURNAL CITATION ABOVE REMARK 4 REMARK 4 1UUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1290014236. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 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; TOCSY; COSY; ROESY 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 : XPLOR/CHARMM REMARK 210 METHOD USED : NOE-RESTRAINED DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRRAINT VIOLATION REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR REMARK 210 SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR REMARK 210 RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR REMARK 210 SPECTRA FOR THE RNA AS ABOUND BY THE LIGAND RBT203 SHOWED REMARK 210 SIMILAR NOE AND CHEMICAL SHIFT PATTERNS TO THE LATTER 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 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 18 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A B 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G B 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A B 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 26 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 28 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 32 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 32 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 33 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 33 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A B 35 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G B 36 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G B 36 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 43 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 43 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES 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 P14 B1046 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UTS RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND REMARK 900 RELATED ID: 1UUI RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND DBREF 1UUD B 17 45 PDB 1UUD 1UUD 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 P14 B1046 57 HETNAM P14 N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL) HETNAM 2 P14 AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE HETSYN P14 RBT203 INHIBITOR FORMUL 2 P14 C16 H31 N7 O2 2+ SITE 1 AC1 9 A B 22 U B 23 G B 26 A B 27 SITE 2 AC1 9 G B 28 A B 35 G B 36 C B 37 SITE 3 AC1 9 U B 38 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