Header list of 2a9x.pdb file
Complete list - 9 20 Bytes
HEADER RNA BINDING PROTEIN/RNA 12-JUL-05 2A9X
TITLE TAR RNA RECOGNITION BY A CYCLIC PEPTIDOMIMETIC OF TAT PROTEIN
CAVEAT 2A9X CHIRALITY ERROR AT CA CENTER OF PRO 13
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BIV TAR RNA;
COMPND 3 CHAIN: 2;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: BIV-2 CYCLIC PEPTIDE;
COMPND 7 CHAIN: 1;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA WAS TRANSCRIBED IN VITRO FROM DNA OLIGONUCLEOTIDE
SOURCE 4 TEMPLATES WITH T7 RNA POLYMERASE PURIFIED IN HOUSE WITH UNLABELED OR
SOURCE 5 13C/15N ENRICHED NTPS (SILANTES) AND PURIFIED BY DENATURING PAGE.;
SOURCE 6 MOL_ID: 2;
SOURCE 7 SYNTHETIC: YES;
SOURCE 8 OTHER_DETAILS: THE BIV-2 PEPTIDE WAS SYNTHESIZED BY SOLID PHASE
SOURCE 9 SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC
KEYWDS NMR; PEPTIDOMIMETICS; PEPTIDE STRUCTURE, RNA RECOGNITION;
KEYWDS 2 IMMUNODEFICIENCY VIRUS; TAR RNA;, RNA BINDING PROTEIN-RNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR T.C.LEEPER,Z.ATHANASSIOU,R.L.DIAS,J.A.ROBINSON,G.VARANI
REVDAT 3 09-MAR-22 2A9X 1 REMARK LINK
REVDAT 2 24-FEB-09 2A9X 1 VERSN
REVDAT 1 01-NOV-05 2A9X 0
JRNL AUTH T.C.LEEPER,Z.ATHANASSIOU,R.L.DIAS,J.A.ROBINSON,G.VARANI
JRNL TITL TAR RNA RECOGNITION BY A CYCLIC PEPTIDOMIMETIC OF TAT
JRNL TITL 2 PROTEIN.
JRNL REF BIOCHEMISTRY V. 44 12362 2005
JRNL REFN ISSN 0006-2960
JRNL PMID 16156649
JRNL DOI 10.1021/BI0510532
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.0, X-PLOR 2.9
REMARK 3 AUTHORS : BRUKER (XWINNMR), SCHWIETERS ET AL (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2A9X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-05.
REMARK 100 THE DEPOSITION ID IS D_1000033668.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 275
REMARK 210 PH : 5; 5
REMARK 210 IONIC STRENGTH : 20 MM NA+; 20 MM NA+
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.8 MM BIV-2 PEPTIDE PLUS
REMARK 210 UNLABELED 0.8 MM BIV TAR RNA, 20
REMARK 210 MM SODIUM ACETATE, D3, PH 5.0,
REMARK 210 100% D2O; 0.8 MM BIV-2 PEPTIDE
REMARK 210 PLUS UNLABELED 0.8 MM BIV TAR
REMARK 210 RNA, 20 MM SODIUM ACETATE, D3,
REMARK 210 PH 5.0, 90% H2O, 10% D2O; 0.6 MM
REMARK 210 BIV-2 PEPTIDE PLUS 13C/15N
REMARK 210 LABELED 0.6 MM BIV TAR RNA, 20
REMARK 210 MM SODIUM ACETATE, D3, PH 5.0,
REMARK 210 100% D2O; 0.6 MM BIV-2 PEPTIDE
REMARK 210 PLUS 13C/15N LABELED 0.6 MM BIV
REMARK 210 TAR RNA, 20 MM SODIUM ACETATE,
REMARK 210 D3, PH 5.0, 90% H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HCCH-COSY; HCCH-TOCSY;
REMARK 210 HNN-COSY; F1FF2F-TYPE 2D TOCSY;
REMARK 210 F1FF2F-TYPE 2D NOESY; 3D 31P
REMARK 210 HETCOR ETC; IPAP-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.3, X-PLOR 2.9, SPARKY
REMARK 210 3.110
REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 2, 1
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 U 2 16 H5 C 2 17 1.11
REMARK 500 O2' G 2 4 H8 G 2 5 1.33
REMARK 500 O4 U 2 16 HH12 ARG 1 5 1.40
REMARK 500 O2' G 2 11 H5'' A 2 13 1.57
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 2 C 2 26 C4' C 2 26 C3' 0.067
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 2 11 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES
REMARK 500 1 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES
REMARK 500 3 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES
REMARK 500 3 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES
REMARK 500 3 A 2 21 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES
REMARK 500 4 U 2 10 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 4 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES
REMARK 500 5 G 2 11 C5' - C4' - C3' ANGL. DEV. = -9.7 DEGREES
REMARK 500 5 A 2 18 C5' - C4' - C3' ANGL. DEV. = -10.2 DEGREES
REMARK 500 5 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.8 DEGREES
REMARK 500 6 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES
REMARK 500 6 A 2 13 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES
REMARK 500 6 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 6 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.9 DEGREES
REMARK 500 6 G 2 22 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES
REMARK 500 7 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 8 A 2 13 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 8 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES
REMARK 500 8 A 2 18 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES
REMARK 500 8 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.5 DEGREES
REMARK 500 9 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES
REMARK 500 9 U 2 16 C5' - C4' - C3' ANGL. DEV. = -9.4 DEGREES
REMARK 500 10 U 2 16 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES
REMARK 500 10 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ARG 1 3 1.18 -64.87
REMARK 500 1 THR 1 4 71.35 26.38
REMARK 500 1 ARG 1 5 149.54 -37.97
REMARK 500 1 LYS 1 7 -43.30 -141.18
REMARK 500 1 ARG 1 8 -159.01 -92.08
REMARK 500 1 PRO 1 13 -122.46 77.65
REMARK 500 2 VAL 1 2 60.91 -150.75
REMARK 500 2 ARG 1 5 101.18 -40.73
REMARK 500 2 PRO 1 13 -126.06 77.15
REMARK 500 3 THR 1 4 54.75 -63.62
REMARK 500 3 PRO 1 13 -121.59 73.67
REMARK 500 4 ARG 1 3 81.30 -55.51
REMARK 500 4 THR 1 4 81.41 -60.90
REMARK 500 4 ARG 1 5 -92.12 -39.34
REMARK 500 4 ARG 1 9 112.63 -165.10
REMARK 500 4 PRO 1 13 -102.38 48.88
REMARK 500 5 ARG 1 3 41.90 -101.90
REMARK 500 5 ARG 1 8 -158.30 -101.00
REMARK 500 5 PRO 1 13 -124.19 80.63
REMARK 500 6 VAL 1 2 84.73 -171.56
REMARK 500 6 ARG 1 8 -152.24 -134.92
REMARK 500 6 PRO 1 13 -127.84 82.58
REMARK 500 7 THR 1 4 85.02 -69.16
REMARK 500 7 ARG 1 5 -168.66 -58.68
REMARK 500 7 ARG 1 9 106.91 -161.29
REMARK 500 7 PRO 1 13 -128.84 84.93
REMARK 500 8 THR 1 4 89.78 -45.09
REMARK 500 8 ARG 1 5 -153.42 -64.80
REMARK 500 8 ARG 1 8 -155.42 -97.92
REMARK 500 8 ARG 1 9 91.87 -176.88
REMARK 500 8 VAL 1 12 86.79 -152.22
REMARK 500 8 PRO 1 13 -131.12 84.96
REMARK 500 9 ARG 1 3 53.37 -145.68
REMARK 500 9 ARG 1 8 -145.88 -94.73
REMARK 500 9 ARG 1 9 100.76 -165.73
REMARK 500 9 VAL 1 12 87.73 -154.42
REMARK 500 9 PRO 1 13 -135.32 81.30
REMARK 500 10 THR 1 4 2.25 -57.67
REMARK 500 10 ARG 1 5 23.62 39.13
REMARK 500 10 ARG 1 8 -155.66 -59.79
REMARK 500 10 ARG 1 9 113.63 -170.42
REMARK 500 10 PRO 1 13 -128.64 85.55
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2A9X 2 4 31 PDB 2A9X 2A9X 4 31
DBREF 2A9X 1 1 14 PDB 2A9X 2A9X 1 14
SEQRES 1 2 28 G G C U C G U G U A G C U
SEQRES 2 2 28 C A U U A G C U C C G A G
SEQRES 3 2 28 C C
SEQRES 1 1 14 ARG VAL ARG THR ARG GLY LYS ARG ARG ILE ARG VAL PRO
SEQRES 2 1 14 PRO
LINK N ARG 1 1 C PRO 1 14 1555 1555 1.31
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 - 9 20 Bytes