Header list of 1uts.pdb file
Complete list - y 5 2 Bytes
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
Complete list - y 5 2 Bytes