Header list of 1uui.pdb file
Complete list - 25 201 Bytes
HEADER HIV-1 19-DEC-03 1UUI
TITLE NMR STRUCTURE OF A SYNTHETIC SMALL MOLECULE, RBT158, BOUND
TITLE 2 TO HIV-1 TAR RNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*
COMPND 3 CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C)-3';
COMPND 4 CHAIN: B;
COMPND 5 FRAGMENT: HIV_1 TAR BULGED STEM LOOP;
COMPND 6 SYNONYM: HIV-1 TAR RNA;
COMPND 7 OTHER_DETAILS: BULGED STEM LOOP REGION FROM 5'LTR OF HIV-1
COMPND 8 MRNA-BINDING SITE FOR TRANSCRIPTIONAL ACTIVATOR PROTEIN
COMPND 9 TAT.
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
SOURCE 4 (CLONE 12);
SOURCE 5 ORGANISM_TAXID: 11679;
SOURCE 6 OTHER_DETAILS: 29 NUCLEOTIDE SEQUENCE COMPRSISING PRIMARY
SOURCE 7 BINDING SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA
SOURCE 8 POLYMERASE OFF OF A DNA TEMPLATE
KEYWDS HIV-1, TAR RNA, DRUG DESIGN, LIGAND-RNA INTERACTION, RNA
KEYWDS 2 BULGE, INHIBITOR
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 2 24-FEB-09 1UUI 1 VERSN
REVDAT 1 12-FEB-04 1UUI 0
JRNL AUTH B.DAVIS,M.AFSHAR,G.VARANI,A.I.H.MURCHIE,J.KARN,
JRNL AUTH 2 G.LENTZEN,M.J.DRYSDALE,J.BOWER,A.J.POTTER,
JRNL AUTH 3 F.ABOUL-ELA
JRNL TITL RATIONAL DESIGN OF INHIBITORS OF HIV-1 TAR RNA
JRNL TITL 2 THROUGH THE STABILISATION OF ELECTROSTATIC "HOT
JRNL TITL 3 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 TYPE-1 TAR RNA REVEALS PRINCIPLES OF RNA
REMARK 1 TITL 3 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 1UUI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-04.
REMARK 100 THE PDBE ID CODE IS EBI-14258.
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; 600; 600; 500
REMARK 210 SPECTROMETER MODEL : DRX800; DRX600; DMX600; AMX500
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
REMARK 210 VIOLATION ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR
REMARK 210 SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA
REMARK 210 INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB
REMARK 210 1995, AS THE NMR SPECTRA FOR THE RNA AS ABOUND BY THE
REMARK 210 LIGAND RBT203 SHOWED SIMILAR NOE AND CHEMICAL SHIFT
REMARK 210 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 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 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 G B 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 G B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 A B 20 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 G B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 G B 21 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 A B 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 G B 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G B 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G B 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G B 28 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 32 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G B 33 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G B 33 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 A B 35 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G B 36 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 G B 36 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 G B 43 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G B 43 N7 - C8 - N9 ANGL. DEV. = 4.5 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 P12 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: 1UUD RELATED DB: PDB
REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND
DBREF 1UUI B 17 45 PDB 1UUI 1UUI 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 P12 B1046 53
HETNAM P12 4-[AMINO(IMINO)METHYL]-1-[2-(3-
HETNAM 2 P12 AMMONIOPROPOXY)-5-METHOXYBENZYL]PIPERAZIN-1-
HETNAM 3 P12 IUM
HETSYN P12 RBT205 INHIBITOR
FORMUL 2 P12 C16 H29 N5 O2
SITE 1 AC1 7 A B 22 U B 23 G B 26 A B 27
SITE 2 AC1 7 C B 37 U B 38 C B 39
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
Complete list - 25 201 Bytes