HEADER RNA 12-JAN-11 2L8H TITLE CHEMICAL PROBE BOUND TO HIV TAR RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV TAR RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: IN VITRO TRANSCRIPTION USING T7 POLYMERASE KEYWDS RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.DAVIDSON,D.BEGLEY,C.LAU,G.VARANI REVDAT 4 15-FEB-23 2L8H 1 SOURCE REMARK LINK REVDAT 3 03-AUG-11 2L8H 1 JRNL REVDAT 2 06-APR-11 2L8H 1 JRNL REVDAT 1 23-MAR-11 2L8H 0 JRNL AUTH A.DAVIDSON,D.W.BEGLEY,C.LAU,G.VARANI JRNL TITL A SMALL-MOLECULE PROBE INDUCES A CONFORMATION IN HIV TAR RNA JRNL TITL 2 CAPABLE OF BINDING DRUG-LIKE FRAGMENTS. JRNL REF J.MOL.BIOL. V. 410 984 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21763501 JRNL DOI 10.1016/J.JMB.2011.03.039 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RDC RESTRAINTS APPLIED AFTER INITIAL REMARK 3 STRUCTURE CALCULATIONS REMARK 4 REMARK 4 2L8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000102088. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277; 298 REMARK 210 PH : 6.6; 6.6 REMARK 210 IONIC STRENGTH : 10 MM POTASSIUM PHOSPHATE; 10 MM REMARK 210 POTASSIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM HIV TAR RNA, 4 MM ARGININE REMARK 210 4-METHOXY-NAPTHYLAMIDE, 99.99% REMARK 210 D2O; 1 MM HIV TAR RNA, 4 MM REMARK 210 ARGININE 4-METHOXY-NAPTHYLAMIDE, REMARK 210 90% H2O, 10% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] HIV TAR RNA, 4 REMARK 210 MM ARGININE 4-METHOXY- REMARK 210 NAPTHYLAMIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-1H NOESY WITH REMARK 210 WATERGATE; 1H-1H TOCSY; HCCH- REMARK 210 COSY; 13C HSQC-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 H2' G A 32 H8 G A 33 1.25 REMARK 500 O2' A A 22 H6 U A 23 1.47 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 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 2 C A 30 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 2 U A 31 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 2 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES REMARK 500 3 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES REMARK 500 4 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES REMARK 500 5 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 6 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 U A 25 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 7 C A 30 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 7 U A 31 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 7 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 U A 25 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 8 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 9 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 U A 25 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 10 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES 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 5 C A 39 0.06 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 ARG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L8H A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17408 RELATED DB: BMRB DBREF 2L8H A 17 45 PDB 2L8H 2L8H 17 45 SEQRES 1 A 29 G G C A G A U C U G A G C SEQRES 2 A 29 C U G G G A G C U C U C U SEQRES 3 A 29 G C C HET ARG A 1 26 HET L8H A 2 23 HETNAM ARG ARGININE HETNAM L8H 4-METHOXYNAPHTHALEN-2-AMINE FORMUL 2 ARG C6 H15 N4 O2 1+ FORMUL 3 L8H C11 H11 N O LINK C ARG A 1 N L8H A 2 1555 1555 1.33 SITE 1 AC1 7 L8H A 2 G A 21 A A 22 U A 23 SITE 2 AC1 7 A A 35 G A 36 C A 37 SITE 1 AC2 5 ARG A 1 C A 30 U A 31 A A 35 SITE 2 AC2 5 G A 36 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