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Database: PDB
Entry: 5TR5
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Original site: 5TR5 
HEADER    LIGASE                                  25-OCT-16   5TR5              
TITLE     SOLUTION STRUCTURE OF SERINE 65 PHOSPHORYLATED UBL DOMAIN FROM PARKIN 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN;                        
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: RESIDUES 1-76;                                             
COMPND   5 SYNONYM: PARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2,PARKINSON       
COMPND   6 DISEASE PROTEIN 2;                                                   
COMPND   7 EC: 6.3.2.-;                                                         
COMPND   8 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: PARK2, PRKN;                                                   
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET SUMO                                  
KEYWDS    PHOSPHORYLATION, PINK1, PARKINSON'S DISEASE, LIGASE                   
EXPDTA    SOLUTION NMR                                                          
NUMMDL    25                                                                    
AUTHOR    J.D.AGUIRRE,K.M.DUNKERLEY,P.MERCIER,G.S.SHAW                          
REVDAT   4   08-JAN-20 5TR5    1       COMPND                                   
REVDAT   3   25-JAN-17 5TR5    1       JRNL                                     
REVDAT   2   04-JAN-17 5TR5    1       JRNL                                     
REVDAT   1   21-DEC-16 5TR5    0                                                
JRNL        AUTH   J.D.AGUIRRE,K.M.DUNKERLEY,P.MERCIER,G.S.SHAW                 
JRNL        TITL   STRUCTURE OF PHOSPHORYLATED UBL DOMAIN AND INSIGHTS INTO     
JRNL        TITL 2 PINK1-ORCHESTRATED PARKIN ACTIVATION.                        
JRNL        REF    PROC. NATL. ACAD. SCI.        V. 114   298 2017              
JRNL        REF  2 U.S.A.                                                       
JRNL        REFN                   ESSN 1091-6490                               
JRNL        PMID   28007983                                                     
JRNL        DOI    10.1073/PNAS.1613040114                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR NIH                                           
REMARK   3   AUTHORS     : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE             
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 5TR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-16.                  
REMARK 100 THE DEPOSITION ID IS D_1000223018.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 7                                  
REMARK 210  IONIC STRENGTH                 : 100                                
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 300 UM [U-15N] PUBL, 25 MM         
REMARK 210                                   HEPES, 100 MM SODIUM CHLORIDE,     
REMARK 210                                   250 UM TCEP, 200 UM DSS, 300 UM    
REMARK 210                                   IMIDAZOLE, 90% H2O/10% D2O; 300    
REMARK 210                                   UM [U-13C] PUBL, 25 MM HEPES,      
REMARK 210                                   100 MM SODIUM CHLORIDE, 250 UM     
REMARK 210                                   TCEP, 200 UM DSS, 300 UM           
REMARK 210                                   IMIDAZOLE, 90% H2O/10% D2O; 400    
REMARK 210                                   UM [U-99% 13C; U-99% 15N] PUBL,    
REMARK 210                                   25 MM HEPES, 100 MM SODIUM         
REMARK 210                                   CHLORIDE, 250 UM TCEP, 200 UM      
REMARK 210                                   DSS, 300 UM IMIDAZOLE, 90% H2O/    
REMARK 210                                   10% D2O; 400 UM PUBL, 25 MM        
REMARK 210                                   HEPES, 100 MM SODIUM CHLORIDE,     
REMARK 210                                   250 UM TCEP, 200 UM DSS, 300 UM    
REMARK 210                                   IMIDAZOLE, 100% D2O                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC     
REMARK 210                                   ALIPHATIC; 2D 1H-13C HSQC          
REMARK 210                                   AROMATIC; 3D HNCA; 3D HNCACB; 3D   
REMARK 210                                   HNCO; 3D C(CO)NH; 3D HCCH-TOCSY;   
REMARK 210                                   2D (HB)CB(CGCD)HD; 3D 1H-13C       
REMARK 210                                   NOESY ALIPHATIC; 3D 1H-13C NOESY   
REMARK 210                                   AROMATIC; 3D 1H-15N NOESY          
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE 8.9, NMRVIEW 8.2.4, VNMR   
REMARK 210                                   3.2, CYANA                         
REMARK 210   METHOD USED                   : NA                                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 25                                 
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: 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: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
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   O    THR A    55     HG   CYS A    59              1.60            
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 HIS A  11     -166.14   -105.38                                   
REMARK 500  1 SEP A  65     -151.86     59.24                                   
REMARK 500  2 SEP A  65     -158.30     53.64                                   
REMARK 500  3 ASN A   8       23.11     45.96                                   
REMARK 500  3 HIS A  11      179.14     66.79                                   
REMARK 500  3 ASP A  53       70.74   -110.71                                   
REMARK 500  3 SEP A  65     -104.39     55.07                                   
REMARK 500  4 HIS A  11     -169.34   -110.85                                   
REMARK 500  4 ASP A  60       91.01     60.34                                   
REMARK 500  4 GLN A  64     -159.67    -84.18                                   
REMARK 500  5 HIS A  11     -157.20   -103.09                                   
REMARK 500  5 GLN A  64     -156.10    -95.62                                   
REMARK 500  5 SEP A  65     -170.41    -66.79                                   
REMARK 500  6 ASP A  60       80.61     63.53                                   
REMARK 500  6 SEP A  65      164.09     80.04                                   
REMARK 500  7 SER A   9       14.63     55.31                                   
REMARK 500  7 SER A  10      -68.77    -90.41                                   
REMARK 500  7 ASP A  60       71.95     58.76                                   
REMARK 500  7 ARG A  75       32.16   -140.59                                   
REMARK 500  8 GLN A  64     -154.78   -120.15                                   
REMARK 500  8 ARG A  75       81.02     57.71                                   
REMARK 500  9 SER A  10     -152.49    -87.16                                   
REMARK 500  9 ALA A  46      -63.58     68.46                                   
REMARK 500 10 GLN A  64      -84.17    -68.47                                   
REMARK 500 11 HIS A  11      -79.89     64.37                                   
REMARK 500 11 ASP A  53       73.01   -102.62                                   
REMARK 500 11 GLN A  64     -160.39    -78.46                                   
REMARK 500 12 HIS A  11      -74.29    -94.50                                   
REMARK 500 12 GLN A  64      -71.46   -128.03                                   
REMARK 500 12 PRO A  73       94.79    -67.17                                   
REMARK 500 13 SER A  10     -146.24    -92.55                                   
REMARK 500 13 ASP A  53       79.68   -113.50                                   
REMARK 500 14 GLN A  64      -76.40    -92.84                                   
REMARK 500 15 SER A  10      -79.21    -67.01                                   
REMARK 500 15 HIS A  11      -58.62   -132.43                                   
REMARK 500 15 ASP A  20       69.24   -101.03                                   
REMARK 500 15 ALA A  46      -66.25     68.66                                   
REMARK 500 15 ASP A  53       74.36   -102.84                                   
REMARK 500 15 GLN A  64     -165.72    -75.39                                   
REMARK 500 16 SER A  10     -158.80    -88.99                                   
REMARK 500 16 ASP A  60       50.41    -69.41                                   
REMARK 500 16 GLN A  64     -155.99   -102.40                                   
REMARK 500 16 SEP A  65     -163.39    -71.52                                   
REMARK 500 16 ARG A  75       76.33     56.80                                   
REMARK 500 17 ASN A   8      -44.83     66.70                                   
REMARK 500 17 SEP A  65     -168.18     57.43                                   
REMARK 500 18 SER A  10     -162.96   -121.43                                   
REMARK 500 18 SEP A  65     -164.74     62.61                                   
REMARK 500 19 ALA A  46      -62.46     68.18                                   
REMARK 500 19 ASP A  53       79.12   -103.83                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      73 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 650                                                                      
REMARK 650 HELIX                                                                
REMARK 650 DETERMINATION METHOD: AUTHOR                                         
REMARK 700                                                                      
REMARK 700 SHEET                                                                
REMARK 700 DETERMINATION METHOD: AUTHOR                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 30197   RELATED DB: BMRB                                 
REMARK 900 SOLUTION STRUCTURE OF SERINE 65 PHOSPHORYLATED UBL DOMAIN FROM       
REMARK 900 PARKIN                                                               
DBREF  5TR5 A    1    76  UNP    O60260   PRKN2_HUMAN      1     76             
SEQRES   1 A   76  MET ILE VAL PHE VAL ARG PHE ASN SER SER HIS GLY PHE          
SEQRES   2 A   76  PRO VAL GLU VAL ASP SER ASP THR SER ILE PHE GLN LEU          
SEQRES   3 A   76  LYS GLU VAL VAL ALA LYS ARG GLN GLY VAL PRO ALA ASP          
SEQRES   4 A   76  GLN LEU ARG VAL ILE PHE ALA GLY LYS GLU LEU ARG ASN          
SEQRES   5 A   76  ASP TRP THR VAL GLN ASN CYS ASP LEU ASP GLN GLN SEP          
SEQRES   6 A   76  ILE VAL HIS ILE VAL GLN ARG PRO TRP ARG LYS                  
MODRES 5TR5 SEP A   65  SER  MODIFIED RESIDUE                                   
HET    SEP  A  65      14                                                       
HETNAM     SEP PHOSPHOSERINE                                                    
HETSYN     SEP PHOSPHONOSERINE                                                  
FORMUL   1  SEP    C3 H8 N O6 P                                                 
HELIX    1 AA1 ILE A   23  GLN A   34  1                                  12    
HELIX    2 AA2 VAL A   56  CYS A   59  1                                   4    
HELIX    3 AA3 LEU A   61  GLN A   64  1                                   4    
SHEET    1 AA1 4 MET A   1  ARG A   6  0                                        
SHEET    2 AA1 4 PHE A  13  VAL A  17  0                                        
SHEET    3 AA1 4 LEU A  41  ILE A  44  1  O  VAL A  67   N  ARG A   6           
SHEET    4 AA1 4 VAL A  67  GLN A  71  0                                        
LINK         C   GLN A  64                 N   SEP A  65     1555   1555  1.33  
LINK         C   SEP A  65                 N   ILE A  66     1555   1555  1.32  
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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