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PDBsum entry 2kbu

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Isomerase PDB id
2kbu
Jmol
Contents
Protein chain
31 a.a.
HEADER    ISOMERASE                               08-DEC-08   2KBU
TITLE     NMR SOLUTION STRUCTURE OF PIN1 WW DOMAIN MUTANT WITH BETA
TITLE    2 TURN MIMIC AT POSITION 12
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-
COMPND   3 INTERACTING 1;
COMPND   4 CHAIN: A;
COMPND   5 FRAGMENT: UNP RESIDUES 6-39;
COMPND   6 SYNONYM: ROTAMASE PIN1, PPIASE PIN1;
COMPND   7 EC: 5.2.1.8;
COMPND   8 ENGINEERED: YES;
COMPND   9 MUTATION: YES;
COMPND  10 OTHER_DETAILS: RESIDUES RSSG REPLACED BY THE BETA-TURN
COMPND  11 MIMIC CFD
SOURCE    MOL_ID: 1;
SOURCE   2 SYNTHETIC: YES;
SOURCE   3 OTHER_DETAILS: RESIDUES RSSG REPLACED BY THE BETA-TURN
SOURCE   4 MIMIC CFD
KEYWDS    BETA SHEET NUCLEATOR, BETA TURN MIMIC, CELL CYCLE,
KEYWDS   2 ISOMERASE, NUCLEUS, PHOSPHOPROTEIN, ROTAMASE
EXPDTA    SOLUTION NMR
NUMMDL    15
AUTHOR    A.A.FULLER,G.BHABHA,D.A.CASE
REVDAT   2   28-JUL-09 2KBU    1       JRNL
REVDAT   1   07-JUL-09 2KBU    0
JRNL        AUTH   A.A.FULLER,D.DU,F.LIU,J.E.DAVOREN,G.BHABHA,G.KROON,
JRNL        AUTH 2 D.A.CASE,H.J.DYSON,E.T.POWERS,P.WIPF,M.GRUEBELE,
JRNL        AUTH 3 J.W.KELLY
JRNL        TITL   EVALUATING BETA-TURN MIMICS AS BETA-SHEET FOLDING
JRNL        TITL 2 NUCLEATORS.
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 106 11067 2009
JRNL        REFN                   ISSN 0027-8424
JRNL        PMID   19541614
JRNL        DOI    10.1073/PNAS.0813012106
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : AMBER
REMARK   3   AUTHORS     : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,
REMARK   3                 DUKE, LUO, ... AND KOLLM
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2KBU COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-08.
REMARK 100 THE RCSB ID CODE IS RCSB100926.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 288.2
REMARK 210  PH                             : 7.0
REMARK 210  IONIC STRENGTH                 : 0
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 0.446 MM WW DOMAIN, 90% H2O/
REMARK 210                                   10% D2O; 0.447 MM WW DOMAIN,
REMARK 210                                   100% D2O
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-1H TOCSY; 2D 1H-1H
REMARK 210                                   COSY; 2D 1H-1H NOESY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 500 MHZ; 600 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE; DRX
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : AMBER
REMARK 210   METHOD USED                   : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 27
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 15
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH ACCEPTABLE
REMARK 210                                   COVALENT GEOMETRY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 001
REMARK 210
REMARK 210 REMARK: SAME EXPERIMENTS ALSO COLLECTED IN D2O WITH SAMPLE-2
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  1 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   4.7 DEGREES
REMARK 500  1 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES
REMARK 500  2 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   4.5 DEGREES
REMARK 500  2 PRO A  29   CA  -  N   -  CD  ANGL. DEV. = -11.0 DEGREES
REMARK 500  3 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   4.7 DEGREES
REMARK 500  3 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES
REMARK 500  3 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   4.7 DEGREES
REMARK 500  5 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   3.9 DEGREES
REMARK 500  6 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES
REMARK 500  6 ARG A  28   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.5 DEGREES
REMARK 500  8 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   4.3 DEGREES
REMARK 500  8 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   5.2 DEGREES
REMARK 500  9 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   4.2 DEGREES
REMARK 500  9 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES
REMARK 500 10 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES
REMARK 500 10 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   3.8 DEGREES
REMARK 500 11 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   5.1 DEGREES
REMARK 500 11 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES
REMARK 500 12 ARG A   9   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.7 DEGREES
REMARK 500 12 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES
REMARK 500 13 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES
REMARK 500 13 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   4.2 DEGREES
REMARK 500 13 ARG A  28   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.5 DEGREES
REMARK 500 14 ARG A   9   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.2 DEGREES
REMARK 500 14 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   4.4 DEGREES
REMARK 500 15 ARG A   9   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES
REMARK 500 15 ARG A  13   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES
REMARK 500 15 ARG A  28   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 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 ASN A  22       -8.60     59.79
REMARK 500  1 PRO A  29     -166.91    -72.97
REMARK 500  2 PRO A  29       61.43     25.62
REMARK 500  3 PRO A   3      176.13    -58.61
REMARK 500  3 PRO A   4      177.82    -59.81
REMARK 500  4 ILE A  20      -50.48   -126.76
REMARK 500  4 ASN A  22      -11.32     57.60
REMARK 500  4 PRO A  29     -165.06    -74.06
REMARK 500  5 PRO A   3      172.98    -54.76
REMARK 500  5 PRO A   4      179.56    -57.51
REMARK 500  5 PRO A  29       48.55    -68.98
REMARK 500  5 SER A  30      -17.00     59.40
REMARK 500  7 PRO A   4     -177.35    -64.58
REMARK 500  7 ASN A  22        5.02     59.76
REMARK 500  7 PRO A  29      172.64    -54.18
REMARK 500  7 SER A  30       37.78    -71.19
REMARK 500  8 PRO A   4     -169.75    -63.77
REMARK 500  8 ASN A  22        6.62     59.83
REMARK 500  8 PRO A  29     -142.82    -73.94
REMARK 500  8 SER A  30       48.15    -64.38
REMARK 500  9 ASN A  22       19.44     52.86
REMARK 500  9 ARG A  28       63.46     34.46
REMARK 500  9 SER A  30        6.57     48.01
REMARK 500 10 PRO A   4      151.97    -47.02
REMARK 500 10 ASN A  22        6.58     54.49
REMARK 500 10 ARG A  28      151.27     60.81
REMARK 500 10 PRO A  29      141.61    -22.94
REMARK 500 10 SER A  30       87.63    -55.55
REMARK 500 11 ASN A  22       -4.17     61.02
REMARK 500 12 ASN A  22      -12.33     60.81
REMARK 500 13 ASN A  22      -10.20     61.61
REMARK 500 13 SER A  30       46.84   -158.92
REMARK 500 14 ILE A  20      -62.40   -109.42
REMARK 500 15 ASN A  22       17.27     53.04
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  6 ARG A  28         0.08    SIDE_CHAIN
REMARK 500 12 ARG A  28         0.12    SIDE_CHAIN
REMARK 500 14 ARG A  28         0.09    SIDE_CHAIN
REMARK 500 15 ARG A  28         0.08    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 CFD A 12
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES RSSG REPLACED BY THE BETA-TURN MIMIC CFD
DBREF  2KBU A    1    31  UNP    Q13526   PIN1_HUMAN       6     39
SEQADV 2KBU     A       UNP  Q13526    ARG    17 SEE REMARK 999
SEQADV 2KBU     A       UNP  Q13526    SER    18 SEE REMARK 999
SEQADV 2KBU     A       UNP  Q13526    SER    19 SEE REMARK 999
SEQADV 2KBU CFD A   12  UNP  Q13526    GLY    20 SEE REMARK 999
SEQADV 2KBU PHE A   26  UNP  Q13526    TRP    34 ENGINEERED
SEQRES   1 A   31  LYS LEU PRO PRO GLY TRP GLU LYS ARG MET SER CFD ARG
SEQRES   2 A   31  VAL TYR TYR PHE ASN HIS ILE THR ASN ALA SER GLN PHE
SEQRES   3 A   31  GLU ARG PRO SER GLY
HET    CFD  A  12      14
HETNAM     CFD (2R,3E,5R)-5-AMINO-2,4-DIMETHYLHEX-3-ENAL
FORMUL   1  CFD    C8 H15 N O
SHEET    1   A 3 TRP A   6  MET A  10  0
SHEET    2   A 3 VAL A  14  ASN A  18 -1  O  TYR A  15   N  ARG A   9
SHEET    3   A 3 SER A  24  GLN A  25 -1  O  GLN A  25   N  TYR A  16
LINK         C   SER A  11                 N   CFD A  12     1555   1555  1.34
LINK         C   CFD A  12                 N   ARG A  13     1555   1555  1.34
SITE     1 AC1  3 MET A  10  SER A  11  ARG A  13
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
      
PROCHECK
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 References