HEADER RNA 28-MAY-02 1LVJ TITLE STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOLAR TITLE 2 INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL SCREENING COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 TRANS ACTIVATING REGION RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 OTHER_DETAILS: IN VITRO TRANSCRIPTION KEYWDS TRANSCRIPTIONAL ACTIVATION, COMPLEX (RNA-DRUG), RNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR Z.DU,K.E.LIND,T.L.JAMES REVDAT 3 23-FEB-22 1LVJ 1 REMARK REVDAT 2 24-FEB-09 1LVJ 1 VERSN REVDAT 1 11-DEC-02 1LVJ 0 JRNL AUTH Z.DU,K.E.LIND,T.L.JAMES JRNL TITL STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION JRNL TITL 2 NANOMOLAR INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL JRNL TITL 3 SCREENING JRNL REF CHEM.BIOL. V. 9 707 2002 JRNL REFN ISSN 1074-5521 JRNL PMID 12079782 JRNL DOI 10.1016/S1074-5521(02)00151-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.6, AMBER 6.0 REMARK 3 AUTHORS : GUNTERT (DYANA), PEARLMAN ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS DETERMINED BY REMARK 3 MULTIDIMENTIONAL HETERONUCLEAR NMR SPECTROSCOPY ON A UNLABELED, REMARK 3 A 15N,13C-LABELED SAMPLE AND THREE TYPE-SPECIFIC (A,G OR C) REMARK 3 LABELED SAMPLES. REMARK 4 REMARK 4 1LVJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016316. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 30 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10 MM SODIUM PHOSPHATE (PH 6.5), REMARK 210 20MM SODIUM CHLORIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D 13C-SEPERATED REMARK 210 NOESY, 3D 15N-SEPERATED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.0 REMARK 210 METHOD USED : SIMULATED ANNEALING STARTING REMARK 210 FROM RANDOM COORDINATES REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST VIOLATIONS AND LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' A A 35 H8 G A 36 1.47 REMARK 500 O2' C A 30 H5'' U A 31 1.52 REMARK 500 O2' G A 33 H5' G A 34 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 8 G A 33 C8 G A 33 N9 -0.066 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 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 21 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 27 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 28 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 32 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 32 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 33 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 33 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 34 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 34 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 36 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 36 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 G A 43 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 43 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 44 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 44 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 20 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 21 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 27 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 G A 28 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 32 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 32 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 33 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 33 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 34 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 34 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 36 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 331 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 9 U A 40 0.10 SIDE CHAIN REMARK 500 11 U A 40 0.11 SIDE CHAIN 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 PMZ A 47 DBREF 1LVJ A 16 46 PDB 1LVJ 1LVJ 16 46 SEQRES 1 A 31 G G C C A G A U C U G A G SEQRES 2 A 31 C C U G G G A G C U C U C SEQRES 3 A 31 U G G C C HET PMZ A 47 45 HETNAM PMZ 1-[10-(3-DIMETHYLAMINO-PROPYL)-10H-PHENOTHIAZIN-2-YL]- HETNAM 2 PMZ ETHANONE HETSYN PMZ ACETYLPROMAZINE FORMUL 2 PMZ C19 H22 N2 O S SITE 1 AC1 7 A A 22 U A 23 C A 24 U A 25 SITE 2 AC1 7 G A 26 C A 39 U A 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