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PDBsum entry 1iyf

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Ligase PDB id
1iyf
Jmol
Contents
Protein chain
76 a.a. *
* Residue conservation analysis
HEADER    LIGASE                                  13-AUG-02   1IYF
TITLE     SOLUTION STRUCTURE OF UBIQUITIN-LIKE DOMAIN OF HUMAN PARKIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PARKIN;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UBIQUITIN-LIKE DOMAIN;
COMPND   5 EC: 6.3.2.19;
COMPND   6 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS;
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PGEX6P3
KEYWDS    UBIQUITIN FOLD, RIKEN STRUCTURAL GENOMICS/PROTEOMICS
KEYWDS   2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, LIGASE
EXPDTA    SOLUTION NMR
NUMMDL    10
AUTHOR    E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA,
AUTHOR   2 H.KAWAHARA,H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO,
AUTHOR   3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT   2   24-FEB-09 1IYF    1       VERSN
REVDAT   1   25-MAR-03 1IYF    0
JRNL        AUTH   E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,
JRNL        AUTH 2 S.YOKOYAMA,S.YAMADA,H.KAWAHARA,H.YOKOSAWA,
JRNL        AUTH 3 N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO
JRNL        TITL   PARKIN BINDS THE RPN10 SUBUNIT OF 26S PROTEASOMES
JRNL        TITL 2 THROUGH ITS UBIQUITIN-LIKE DOMAIN
JRNL        REF    EMBO REP.                     V.   4   301 2003
JRNL        REFN                   ISSN 1469-221X
JRNL        PMID   12634850
JRNL        DOI    10.1038/SJ.EMBOR.EMBOR764
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.1
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL
REMARK   3  OF 720 RESTRAINTS, 489 ARE NOE-DERIVED DISTANCE CONSTRAINTS,
REMARK   3  82 DIHEDRAL ANGLE RESTRAINTS, 129 RESIDUAL DIPOLAR COUPLING
REMARK   3  CONSTRAINTS, 20 DISTANCE RESTRAINTS FOR HYDROGEN BONDS.
REMARK   4
REMARK   4 1IYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-02.
REMARK 100 THE RCSB ID CODE IS RCSB005405.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 303; 310
REMARK 210  PH                             : 6.0; 6.0
REMARK 210  IONIC STRENGTH                 : 0.3; 0.3
REMARK 210  PRESSURE                       : 1ATM; 1ATM
REMARK 210  SAMPLE CONTENTS                : 0.1MM PARKIN UBIQUITIN-LIKE
REMARK 210                                   DOMAIN U-15N, 13C; 50MM
REMARK 210                                   POTASSIUM PHOSPHATE BUFFER;
REMARK 210                                   0.1MM PARKIN UBIQUITIN-LIKE
REMARK 210                                   DOMAIN U-15N, 13C; 50MM
REMARK 210                                   POTASSIUM PHOSPHATE BUFFER
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_
REMARK 210                                   15N-SEPARATED_NOESY, 2D_1H-
REMARK 210                                   COUPLED_1H-15N_HSQC
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ
REMARK 210  SPECTROMETER MODEL             : DRX
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : XWINNMR 2.6, CNS 1.1
REMARK 210   METHOD USED                   : DISTANCE GEOMETRY, SIMULATED
REMARK 210                                   ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST
REMARK 210                                   ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210  SPECTROSCOPY.
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465   MODELS 1-10
REMARK 465     RES C SSSEQI
REMARK 465     GLY A    -4
REMARK 465     PRO A    -3
REMARK 465     LEU A    -2
REMARK 465     GLY A    -1
REMARK 465     SER A     0
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   O    ILE A    44     O    HIS A    68              2.10
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   8       69.22    -63.01
REMARK 500  1 HIS A  11      115.51   -160.52
REMARK 500  1 VAL A  17      154.60    177.10
REMARK 500  1 THR A  21      154.39    -37.18
REMARK 500  1 SER A  22      142.73    -18.26
REMARK 500  1 ILE A  23      -39.43    -39.70
REMARK 500  1 VAL A  30      -71.78    -58.46
REMARK 500  1 PRO A  37     -152.24    -65.17
REMARK 500  1 ALA A  38      -70.44   -106.54
REMARK 500  1 LEU A  41     -143.33    -82.67
REMARK 500  1 ALA A  46       36.28     23.62
REMARK 500  1 LEU A  50       87.81     -9.77
REMARK 500  1 VAL A  56     -133.45    -70.66
REMARK 500  1 CYS A  59      -78.66    -81.36
REMARK 500  1 ASP A  60       76.02   -168.73
REMARK 500  2 ASN A   8       68.90    -63.73
REMARK 500  2 VAL A  17      152.40    178.88
REMARK 500  2 THR A  21      150.58    -33.51
REMARK 500  2 SER A  22      142.99    -17.30
REMARK 500  2 ILE A  23      -39.99    -39.69
REMARK 500  2 VAL A  30      -73.41    -58.78
REMARK 500  2 PRO A  37     -148.87    -66.30
REMARK 500  2 ALA A  38      -68.02   -105.31
REMARK 500  2 GLN A  40      -76.31    -53.20
REMARK 500  2 LEU A  41     -138.36    -84.74
REMARK 500  2 ALA A  46       34.90     26.03
REMARK 500  2 LEU A  50       89.51    -14.52
REMARK 500  2 VAL A  56     -133.53    -82.29
REMARK 500  2 CYS A  59      -76.99    -96.71
REMARK 500  2 ASP A  60       76.65   -169.94
REMARK 500  3 ASN A   8       69.39    -63.91
REMARK 500  3 VAL A  17      157.59    175.41
REMARK 500  3 THR A  21      153.69    -35.19
REMARK 500  3 SER A  22      144.27    -16.62
REMARK 500  3 VAL A  30      -73.53    -61.88
REMARK 500  3 PRO A  37     -147.57    -67.04
REMARK 500  3 ALA A  38      -69.82   -105.96
REMARK 500  3 GLN A  40      -77.32    -49.02
REMARK 500  3 LEU A  41     -124.71    -81.94
REMARK 500  3 ALA A  46       37.86     26.87
REMARK 500  3 LEU A  50      107.64    -25.05
REMARK 500  3 VAL A  56     -135.01    -82.26
REMARK 500  3 CYS A  59      -79.10   -106.22
REMARK 500  3 ASP A  60       76.46   -165.39
REMARK 500  4 ASN A   8       68.53    -64.13
REMARK 500  4 VAL A  17      154.71    178.99
REMARK 500  4 THR A  21      152.42    -34.35
REMARK 500  4 SER A  22      143.14    -18.87
REMARK 500  4 VAL A  30      -74.01    -59.05
REMARK 500  4 PRO A  37     -145.19    -68.20
REMARK 500  4 ALA A  38      -65.68   -104.58
REMARK 500  4 GLN A  40      -85.26    -43.95
REMARK 500  4 LEU A  41     -113.89    -94.19
REMARK 500  4 ALA A  46       38.02     25.21
REMARK 500  4 LEU A  50       87.94    -10.89
REMARK 500  4 VAL A  56     -134.36    -78.63
REMARK 500  4 CYS A  59      -78.17    -96.09
REMARK 500  4 ASP A  60       76.67   -169.27
REMARK 500  5 ASN A   8       71.45    -59.28
REMARK 500  5 VAL A  17      152.73    178.86
REMARK 500  5 THR A  21      154.32    -35.34
REMARK 500  5 SER A  22      142.79    -18.12
REMARK 500  5 VAL A  30      -75.01    -57.12
REMARK 500  5 PRO A  37     -148.35    -70.03
REMARK 500  5 GLN A  40       92.59    -56.27
REMARK 500  5 LEU A  41     -161.16    -69.90
REMARK 500  5 ARG A  42       44.74     70.58
REMARK 500  5 ALA A  46       35.79     27.41
REMARK 500  5 LEU A  50       88.24    -14.14
REMARK 500  5 VAL A  56     -136.88    -82.89
REMARK 500  5 CYS A  59      -78.33   -104.08
REMARK 500  5 ASP A  60       77.60   -167.04
REMARK 500  6 ASN A   8       71.53    -66.38
REMARK 500  6 SER A   9     -160.77   -163.93
REMARK 500  6 SER A  10      177.09    -49.41
REMARK 500  6 THR A  21      153.96    -32.79
REMARK 500  6 SER A  22      143.95    -20.69
REMARK 500  6 VAL A  30      -74.01    -67.03
REMARK 500  6 PRO A  37     -142.36    -66.62
REMARK 500  6 ALA A  38      -73.07   -104.68
REMARK 500  6 LEU A  41     -138.74    -83.20
REMARK 500  6 ALA A  46       35.84     24.25
REMARK 500  6 LEU A  50       97.09    -21.46
REMARK 500  6 VAL A  56     -137.35    -83.81
REMARK 500  6 CYS A  59      -77.47   -101.45
REMARK 500  6 ASP A  60       78.53   -165.68
REMARK 500  6 VAL A  70       74.31   -104.09
REMARK 500  7 ASN A   8       70.44    -58.43
REMARK 500  7 VAL A  17     -169.33   -167.37
REMARK 500  7 THR A  21      175.92    -40.19
REMARK 500  7 SER A  22      154.93    -40.18
REMARK 500  7 GLN A  25      -71.30    -58.82
REMARK 500  7 VAL A  30      -74.57    -62.09
REMARK 500  7 PRO A  37     -140.42    -65.48
REMARK 500  7 ALA A  38      -74.89   -110.80
REMARK 500  7 LEU A  41     -136.25    -91.83
REMARK 500  7 ALA A  46       31.85     77.21
REMARK 500  7 LEU A  50       82.16    -14.64
REMARK 500  7 VAL A  56     -129.49    -51.65
REMARK 500  7 CYS A  59      -72.15    -63.73
REMARK 500  7 ASP A  60       74.94   -166.40
REMARK 500  7 GLN A  71       60.51   -118.57
REMARK 500  8 ASN A   8       72.72    -64.46
REMARK 500  8 SER A   9     -161.15   -163.76
REMARK 500  8 SER A  10      175.59    -49.38
REMARK 500  8 VAL A  17      156.03    179.61
REMARK 500  8 THR A  21      154.75    -33.17
REMARK 500  8 SER A  22      143.67    -20.63
REMARK 500  8 VAL A  30      -72.48    -55.42
REMARK 500  8 PRO A  37     -149.79    -66.72
REMARK 500  8 ALA A  38      -69.90   -105.83
REMARK 500  8 GLN A  40      -73.01    -52.26
REMARK 500  8 LEU A  41     -135.03    -82.13
REMARK 500  8 ALA A  46       37.91     22.53
REMARK 500  8 LEU A  50       97.46    -22.70
REMARK 500  8 VAL A  56     -133.47    -81.81
REMARK 500  8 CYS A  59      -78.03    -95.90
REMARK 500  8 ASP A  60       76.01   -168.41
REMARK 500  9 ASN A   8       71.92    -66.76
REMARK 500  9 SER A   9     -159.43   -163.91
REMARK 500  9 SER A  10      175.80    -48.95
REMARK 500  9 VAL A  17     -166.43   -167.84
REMARK 500  9 THR A  21      169.45    -36.14
REMARK 500  9 SER A  22      148.20    -33.88
REMARK 500  9 VAL A  30      -75.75    -57.67
REMARK 500  9 PRO A  37     -147.30    -63.51
REMARK 500  9 ALA A  38      -77.78   -108.79
REMARK 500  9 GLN A  40      -71.10    -46.43
REMARK 500  9 LEU A  41     -138.60    -90.12
REMARK 500  9 ALA A  46       28.69     40.61
REMARK 500  9 VAL A  56     -140.55    -79.88
REMARK 500  9 CYS A  59      -73.67    -84.72
REMARK 500  9 ASP A  60       84.14   -170.66
REMARK 500 10 ASN A   8      178.09    -42.76
REMARK 500 10 SER A   9       79.86    -49.17
REMARK 500 10 VAL A  17      156.35    176.39
REMARK 500 10 THR A  21      151.27    -34.09
REMARK 500 10 SER A  22      143.92    -17.96
REMARK 500 10 VAL A  30      -74.09    -62.53
REMARK 500 10 PRO A  37     -144.20    -66.93
REMARK 500 10 ALA A  38      -68.05   -107.09
REMARK 500 10 GLN A  40      -81.96    -48.53
REMARK 500 10 LEU A  41     -126.18    -87.33
REMARK 500 10 ALA A  46       37.89     26.62
REMARK 500 10 LEU A  50      103.14    -21.66
REMARK 500 10 VAL A  56     -132.82    -80.75
REMARK 500 10 CYS A  59      -78.24    -97.21
REMARK 500 10 ASP A  60       76.39   -168.68
REMARK 500 10 GLN A  71       70.69   -117.39
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5500   RELATED DB: BMRB
REMARK 900 5500 IS CHEMICAL SHIFT
REMARK 900 RELATED ID: MY_001000012.1   RELATED DB: TARGETDB
DBREF  1IYF A    1    76  UNP    O60260   PRKN2_HUMAN      1     76
SEQADV 1IYF GLY A   -4  UNP  O60260              CLONING ARTIFACT
SEQADV 1IYF PRO A   -3  UNP  O60260              CLONING ARTIFACT
SEQADV 1IYF LEU A   -2  UNP  O60260              CLONING ARTIFACT
SEQADV 1IYF GLY A   -1  UNP  O60260              CLONING ARTIFACT
SEQADV 1IYF SER A    0  UNP  O60260              CLONING ARTIFACT
SEQRES   1 A   81  GLY PRO LEU GLY SER MET ILE VAL PHE VAL ARG PHE ASN
SEQRES   2 A   81  SER SER HIS GLY PHE PRO VAL GLU VAL ASP SER ASP THR
SEQRES   3 A   81  SER ILE PHE GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN
SEQRES   4 A   81  GLY VAL PRO ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY
SEQRES   5 A   81  LYS GLU LEU ARG ASN ASP TRP THR VAL GLN ASN CYS ASP
SEQRES   6 A   81  LEU ASP GLN GLN SER ILE VAL HIS ILE VAL GLN ARG PRO
SEQRES   7 A   81  TRP ARG LYS
HELIX    1   1 SER A   22  GLN A   34  1                                  13
HELIX    2   2 VAL A   56  LEU A   61  1                                   6
SHEET    1   A 5 HIS A  11  VAL A  15  0
SHEET    2   A 5 ILE A   2  PHE A   7 -1  N  VAL A   5   O  PHE A  13
SHEET    3   A 5 GLN A  64  VAL A  70  1  O  ILE A  69   N  ARG A   6
SHEET    4   A 5 ARG A  42  PHE A  45 -1  N  ARG A  42   O  VAL A  70
SHEET    5   A 5 LYS A  48  GLU A  49 -1  O  LYS A  48   N  PHE A  45
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
Go to PROCHECK summary
 References