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Database: PDB
Entry: 2K8B
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Original site: 2K8B 
HEADER    PROTEIN BINDING                         04-SEP-08   2K8B              
TITLE     SOLUTION STRUCTURE OF PLAA FAMILY UBIQUITIN BINDING DOMAIN (PFUC) CIS 
TITLE    2 ISOMER IN COMPLEX WITH UBIQUITIN                                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UBIQUITIN;                                                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MOL_ID: 2;                                                           
COMPND   6 MOLECULE: PHOSPHOLIPASE A-2-ACTIVATING PROTEIN;                      
COMPND   7 CHAIN: B;                                                            
COMPND   8 FRAGMENT: UNP RESIDUES 386-465;                                      
COMPND   9 SYNONYM: PLA2P, PLAP;                                                
COMPND  10 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC;                
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PET-22B;                                   
SOURCE  10 MOL_ID: 2;                                                           
SOURCE  11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  12 ORGANISM_COMMON: HUMAN;                                              
SOURCE  13 ORGANISM_TAXID: 9606;                                                
SOURCE  14 GENE: PLAA, PLAP;                                                    
SOURCE  15 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE  16 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE  17 EXPRESSION_SYSTEM_VECTOR: PET-32M                                    
KEYWDS    UBIQUITIN IN COMPLEX WITH PFUC CIS ISOMER, CYTOPLASM, NUCLEUS,        
KEYWDS   2 PHOSPHOPROTEIN, UBL CONJUGATION, WD REPEAT, PROTEIN BINDING          
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    Q.S.FU,C.J.ZHOU,H.C.GAO,D.H.LIN,H.Y.HU                                
REVDAT   4   16-MAR-22 2K8B    1       REMARK                                   
REVDAT   3   28-JUL-09 2K8B    1       JRNL                                     
REVDAT   2   14-JUL-09 2K8B    1       JRNL                                     
REVDAT   1   05-MAY-09 2K8B    0                                                
JRNL        AUTH   Q.S.FU,C.J.ZHOU,H.C.GAO,Y.J.JIANG,Z.R.ZHOU,J.HONG,W.M.YAO,   
JRNL        AUTH 2 A.X.SONG,D.H.LIN,H.Y.HU                                      
JRNL        TITL   STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY A NOVEL DOMAIN 
JRNL        TITL 2 FROM HUMAN PHOSPHOLIPASE A2-ACTIVATING PROTEIN.              
JRNL        REF    J.BIOL.CHEM.                  V. 284 19043 2009              
JRNL        REFN                   ISSN 0021-9258                               
JRNL        PMID   19423704                                                     
JRNL        DOI    10.1074/JBC.M109.009126                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED WITH       
REMARK   3  HADDOCK BY NMR RESTRAINT-GUIDED DOCKING                             
REMARK   4                                                                      
REMARK   4 2K8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-08.                  
REMARK 100 THE DEPOSITION ID IS D_1000100802.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 50MM NACL                          
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.2 MM UBIQUITIN, 90% H2O, 10%     
REMARK 210                                   D2O; 0.2 MM PFUC_CIS, 90% H2O,     
REMARK 210                                   10% D2O                            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC                     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : UNITY                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NULL                               
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 1000                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : 10 STRUCTURES FOR LOWEST ENERGY    
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: A, 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: 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   OD1  ASP B   108     HZ1  LYS B   112              1.57            
REMARK 500   HZ3  LYS B    56     OD1  ASP B    65              1.58            
REMARK 500   HZ1  LYS A     6     OD1  ASP B    71              1.58            
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 B  50       26.68   -145.77                                   
REMARK 500  1 GLN B  51       35.23    -90.34                                   
REMARK 500  1 GLN B  52       59.58    -90.44                                   
REMARK 500  1 GLU B  60      -67.74     65.38                                   
REMARK 500  1 ASN B  73      -42.98    177.66                                   
REMARK 500  1 SER B  86       49.19   -108.08                                   
REMARK 500  1 ASP B 101       79.16     62.56                                   
REMARK 500  1 MET B 122       33.55    -92.76                                   
REMARK 500  1 LEU B 123      -45.00   -141.67                                   
REMARK 500  1 LEU B 125     -151.34     60.32                                   
REMARK 500  2 ASN B  50       11.71   -154.52                                   
REMARK 500  2 GLU B  60      -75.88     64.14                                   
REMARK 500  2 ASP B  65      -71.66    -67.83                                   
REMARK 500  2 ASN B  73      -44.01    177.08                                   
REMARK 500  2 GLN B 121      -88.73     40.89                                   
REMARK 500  2 LEU B 123      -74.46   -128.57                                   
REMARK 500  2 LEU B 125     -146.97    -99.95                                   
REMARK 500  3 GLU A  34      -72.17   -109.66                                   
REMARK 500  3 ALA A  46       19.38     59.90                                   
REMARK 500  3 GLN B  51       36.44    -78.19                                   
REMARK 500  3 GLU B  60      -92.04     57.23                                   
REMARK 500  3 ASP B  65      -71.56    -60.86                                   
REMARK 500  3 ASN B  73      -45.96   -175.68                                   
REMARK 500  3 MET B 122       35.75    -90.66                                   
REMARK 500  3 LEU B 123      -53.89   -134.75                                   
REMARK 500  3 LEU B 125     -155.36     66.18                                   
REMARK 500  4 ASN B  50       23.84   -151.13                                   
REMARK 500  4 GLN B  51       30.79    -94.17                                   
REMARK 500  4 GLU B  60      -82.10     61.86                                   
REMARK 500  4 ASP B  65      -78.54    -63.66                                   
REMARK 500  4 ASN B  73      -50.52   -174.21                                   
REMARK 500  4 SER B  86       59.65   -109.83                                   
REMARK 500  4 ASP B 101       70.91     59.96                                   
REMARK 500  4 LEU B 125     -159.64     59.37                                   
REMARK 500  5 THR A   7     -166.03    -79.33                                   
REMARK 500  5 LYS A  33      -73.33    -81.49                                   
REMARK 500  5 GLU B  60      -84.69     60.45                                   
REMARK 500  5 ASP B  65      -70.08    -63.60                                   
REMARK 500  5 ASN B  73      -59.19   -179.91                                   
REMARK 500  5 SER B  86       31.53    -99.45                                   
REMARK 500  5 ASP B  87     -162.61   -116.05                                   
REMARK 500  5 LEU B 125     -141.45     59.81                                   
REMARK 500  6 GLU A  34     -162.83   -105.17                                   
REMARK 500  6 GLU B  60      -82.16     62.70                                   
REMARK 500  6 ASN B  73      -49.32   -176.46                                   
REMARK 500  6 ASP B 101       78.21     58.38                                   
REMARK 500  6 LEU B 125     -148.50     65.45                                   
REMARK 500  7 LEU A  71     -165.46   -101.17                                   
REMARK 500  7 GLN B  52      102.61     72.43                                   
REMARK 500  7 GLU B  60       17.84     54.81                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      82 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2K89   RELATED DB: PDB                                   
REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN-BINDING DOMAIN PLAA (PFUC, GLY76-    
REMARK 900 PRO77 CIS ISOMER)                                                    
REMARK 900 RELATED ID: 2K8A   RELATED DB: PDB                                   
REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN-BINDING DOMAIN PLAA (PFUC, GLY76-    
REMARK 900 PRO77 TRANS ISOMER)                                                  
REMARK 900 RELATED ID: 2K8C   RELATED DB: PDB                                   
REMARK 900 SOLUTION STRUCTURE OF PLAA FAMILY UBIQUITIN BINDING DOMAIN (PFUC)    
REMARK 900 TRANS ISOMER IN COMPLEX WITH UBIQUITIN                               
DBREF  2K8B A    1    76  UNP    P62988   UBIQ_HUMAN       1     76             
DBREF  2K8B B   49   128  UNP    Q9Y263   PLAP_HUMAN     386    465             
SEQRES   1 A   76  MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE          
SEQRES   2 A   76  THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL          
SEQRES   3 A   76  LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP          
SEQRES   4 A   76  GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP          
SEQRES   5 A   76  GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER          
SEQRES   6 A   76  THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY                  
SEQRES   1 B   80  ALA ASN GLN GLN THR SER GLY LYS VAL LEU TYR GLU GLY          
SEQRES   2 B   80  LYS GLU PHE ASP TYR VAL PHE SER ILE ASP VAL ASN GLU          
SEQRES   3 B   80  GLY GLY PRO SER TYR LYS LEU PRO TYR ASN THR SER ASP          
SEQRES   4 B   80  ASP PRO TRP LEU THR ALA TYR ASN PHE LEU GLN LYS ASN          
SEQRES   5 B   80  ASP LEU ASN PRO MET PHE LEU ASP GLN VAL ALA LYS PHE          
SEQRES   6 B   80  ILE ILE ASP ASN THR LYS GLY GLN MET LEU GLY LEU GLY          
SEQRES   7 B   80  ASN PRO                                                      
HELIX    1   1 THR A   22  GLU A   34  1                                  13    
HELIX    2   2 ASP B   88  ASP B  101  1                                  14    
HELIX    3   3 PRO B  104  GLY B  120  1                                  17    
SHEET    1   A 5 THR A  12  GLU A  16  0                                        
SHEET    2   A 5 GLN A   2  THR A   7 -1  N  VAL A   5   O  ILE A  13           
SHEET    3   A 5 THR A  66  LEU A  71  1  O  LEU A  67   N  LYS A   6           
SHEET    4   A 5 GLN A  41  PHE A  45 -1  N  ARG A  42   O  VAL A  70           
SHEET    5   A 5 LYS A  48  GLN A  49 -1  O  LYS A  48   N  PHE A  45           
SHEET    1   B 2 VAL B  57  TYR B  59  0                                        
SHEET    2   B 2 LYS B  62  PHE B  64 -1  O  LYS B  62   N  TYR B  59           
SHEET    1   C 2 TYR B  66  ILE B  70  0                                        
SHEET    2   C 2 TYR B  79  TYR B  83 -1  O  TYR B  83   N  TYR B  66           
CISPEP   1 GLY B   76    PRO B   77          1        -0.43                     
CISPEP   2 GLY B   76    PRO B   77          2        -0.14                     
CISPEP   3 GLY B   76    PRO B   77          3        -1.20                     
CISPEP   4 GLY B   76    PRO B   77          4        -0.83                     
CISPEP   5 GLY B   76    PRO B   77          5        -0.21                     
CISPEP   6 GLY B   76    PRO B   77          6        -0.20                     
CISPEP   7 GLY B   76    PRO B   77          7        -0.75                     
CISPEP   8 GLY B   76    PRO B   77          8         0.64                     
CISPEP   9 GLY B   76    PRO B   77          9        -0.14                     
CISPEP  10 GLY B   76    PRO B   77         10        -0.27                     
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                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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