HEADER    LIGASE                                  27-OCT-03   1UR6              
TITLE     NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2;                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: UBCH5B, UBIQUITIN CARRIER PROTEIN, E2(17)KB 2;              
COMPND   5 EC: 6.3.2.19;                                                        
COMPND   6 MOL_ID: 2;                                                           
COMPND   7 MOLECULE: POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP;                
COMPND   8 CHAIN: B;                                                            
COMPND   9 FRAGMENT: RING FINGER, RESIDUES 12-63;                               
COMPND  10 SYNONYM: CNOT4, NOT4H                                                
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 MOL_ID: 2;                                                           
SOURCE   6 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   7 ORGANISM_COMMON: HUMAN;                                              
SOURCE   8 ORGANISM_TAXID: 9606                                                 
KEYWDS    LIGASE, UBIQUITIN CONJUGATING ENZYME, UBIQUITIN LIGASE, RING FINGER   
KEYWDS   2 PROTEIN, CCR4-NOT COMPLEX, TRANSCRIPTION REGULATION                  
EXPDTA    SOLUTION NMR; THEORETICAL MODEL                                       
NUMMDL    5                                                                     
AUTHOR    C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,F.M.A.VAN SCHAIK,              
AUTHOR   2 H.TH.M.TIMMERS,R.BOELENS                                             
REVDAT   3   15-MAY-24 1UR6    1       REMARK LINK                              
REVDAT   2   24-FEB-09 1UR6    1       VERSN                                    
REVDAT   1   07-MAY-04 1UR6    0                                                
JRNL        AUTH   C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,F.M.A.VAN SCHAIK,     
JRNL        AUTH 2 H.T.M.TIMMERS,R.BOELENS                                      
JRNL        TITL   STRUCTURAL MODEL OF THE UBCH5B/CNOT4 COMPLEX REVEALED BY     
JRNL        TITL 2 COMBINING NMR, MUTAGENESIS, AND DOCKING APPROACHES.          
JRNL        REF    STRUCTURE                     V.  12   633 2004              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   15062086                                                     
JRNL        DOI    10.1016/J.STR.2004.03.004                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-             
REMARK   3                 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,  
REMARK   3                 SIMONSON,WARREN                                      
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: REFINEMENT DETAILS AS DESCIRIBED IN C.    
REMARK   3  DOMINGUEZ ET AL. (2003), J.AM.CHEM.SOC, 125, P1731                  
REMARK   4                                                                      
REMARK   4 1UR6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-03.                  
REMARK 100 THE DEPOSITION ID IS D_1290013704.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : NULL                               
REMARK 210  PH                             : NULL                               
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : NULL                               
REMARK 210  SAMPLE CONTENTS                : NULL                               
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : NULL                               
REMARK 210  SPECTROMETER FIELD STRENGTH    : NULL                               
REMARK 210  SPECTROMETER MODEL             : NULL                               
REMARK 210  SPECTROMETER MANUFACTURER      : NULL                               
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NULL                               
REMARK 210   METHOD USED                   : NULL                               
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : NULL                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 5                                  
REMARK 210 CONFORMERS, SELECTION CRITERIA  : NULL                               
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
REMARK 210                                                                      
REMARK 210 REMARK: NONE                                                         
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 220                                                                      
REMARK 220 EXPERIMENTAL DETAILS                                                 
REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
REMARK 220                                                                      
REMARK 220 REMARK: THIS THEORETICAL MODEL ENTRY WAS NOT ANNOTATED AND NOT       
REMARK 220         VALIDATED BY THE WWPDB STAFF AND THEREFORE MAY NOT CONFORM   
REMARK 220         TO THE PDB FORMAT.                                           
REMARK 225                                                                      
REMARK 225 THEORETICAL MODEL                                                    
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE.           
REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND                
REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE                   
REMARK 225 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 400                                                                      
REMARK 400 COMPOUND                                                             
REMARK 400 CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS     
REMARK 400  ATP + UBIQUITIN + PROTEIN LYSINE = AMP + DIPHOSPHATE + PROTEIN      
REMARK 400   N-UBIQUITYLLYSINE.                                                 
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   HA   ALA A     2     HB2  CYS B    17              1.31            
REMARK 500   HZ2  LYS A    63     OD2  ASP B    48              1.56            
REMARK 500   OE2  GLU A   140     HZ2  LYS A   144              1.59            
REMARK 500   H3   MET A     1     OE2  GLU B    19              1.59            
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 PRO A  18     -157.27    -70.01                                   
REMARK 500  1 GLN A  20      -48.54     74.95                                   
REMARK 500  1 GLN A  34       65.53   -108.98                                   
REMARK 500  1 VAL A  49       88.82   -162.58                                   
REMARK 500  1 PRO A  61       32.51    -83.36                                   
REMARK 500  1 PHE A  62      -33.81   -148.73                                   
REMARK 500  1 GLN A  92     -164.11     66.55                                   
REMARK 500  1 TRP A  93     -176.23   -171.66                                   
REMARK 500  1 PRO A  95      -84.82    -15.03                                   
REMARK 500  1 ASP A 112       93.56     61.74                                   
REMARK 500  1 PRO A 113      178.75    -59.02                                   
REMARK 500  1 PRO A 118     -115.73    -95.66                                   
REMARK 500  1 PHE B  40       33.23    -77.15                                   
REMARK 500  1 CYS B  41      -47.67   -145.32                                   
REMARK 500  1 ALA B  55       24.86   -140.45                                   
REMARK 500  1 CYS B  56      -28.08   -148.18                                   
REMARK 500  1 ARG B  57       -1.38     72.47                                   
REMARK 500  2 ALA A   2       57.57   -152.20                                   
REMARK 500  2 ALA A  19      112.46   -171.94                                   
REMARK 500  2 GLN A  20      -28.76     73.32                                   
REMARK 500  2 PRO A  44       39.26    -75.55                                   
REMARK 500  2 VAL A  49       85.07   -163.17                                   
REMARK 500  2 PRO A  57     -154.34    -80.08                                   
REMARK 500  2 PHE A  62      -37.39   -140.44                                   
REMARK 500  2 SER A  91       62.99     63.47                                   
REMARK 500  2 GLN A  92      101.17     67.05                                   
REMARK 500  2 ASP A 112       88.49     64.15                                   
REMARK 500  2 PRO A 113      172.93    -58.32                                   
REMARK 500  2 PRO A 118     -135.24    -87.02                                   
REMARK 500  2 PRO B  15      -67.09    -22.31                                   
REMARK 500  2 ILE B  37     -157.34   -129.49                                   
REMARK 500  2 PHE B  40       35.47    -87.36                                   
REMARK 500  2 CYS B  41      -50.75   -149.61                                   
REMARK 500  2 CYS B  56      -21.09    139.45                                   
REMARK 500  3 VAL A  49       57.32   -150.38                                   
REMARK 500  3 PRO A  57     -158.81    -75.02                                   
REMARK 500  3 PRO A  61       36.56    -83.20                                   
REMARK 500  3 PHE A  62      -54.61   -146.60                                   
REMARK 500  3 GLN A  92      110.64     69.46                                   
REMARK 500  3 LEU A  97     -151.02   -140.15                                   
REMARK 500  3 ASP A 112       79.62     60.36                                   
REMARK 500  3 PRO A 113      177.02    -59.40                                   
REMARK 500  3 PRO A 118     -118.96    -86.87                                   
REMARK 500  3 CYS B  17      -24.37   -156.26                                   
REMARK 500  3 MET B  18       31.40     75.15                                   
REMARK 500  3 TYR B  35      112.06   -160.24                                   
REMARK 500  3 ARG B  46       42.14    -90.90                                   
REMARK 500  3 THR B  47      -53.81   -156.13                                   
REMARK 500  3 GLU B  49     -165.99    -79.30                                   
REMARK 500  3 CYS B  56       -5.52     95.42                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      88 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN B  79  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS B  14   SG                                                     
REMARK 620 2 CYS B  17   SG   81.2                                              
REMARK 620 3 CYS B  38   SG   86.2 156.9                                        
REMARK 620 4 CYS B  41   SG   84.5  79.7  79.9                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN B  80  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS B  31   SG                                                     
REMARK 620 2 CYS B  33   SG   79.9                                              
REMARK 620 3 CYS B  53   SG   88.9  85.8                                        
REMARK 620 4 CYS B  56   SG  170.2  98.2  81.3                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 79                   
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 80                   
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1E4U   RELATED DB: PDB                                   
REMARK 900 N-TERMINAL RING FINGER DOMAIN OF HUMAN NOT-4                         
DBREF  1UR6 A    1   147  UNP    P51669   UB5B_HUMAN       1    147             
DBREF  1UR6 B   12    63  UNP    O95628   O95628          12     63             
SEQRES   1 A  147  MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU          
SEQRES   2 A  147  ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL          
SEQRES   3 A  147  GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY          
SEQRES   4 A  147  PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU          
SEQRES   5 A  147  THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO          
SEQRES   6 A  147  LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE          
SEQRES   7 A  147  ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SER          
SEQRES   8 A  147  GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU          
SEQRES   9 A  147  SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP          
SEQRES  10 A  147  PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP          
SEQRES  11 A  147  ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN          
SEQRES  12 A  147  LYS TYR ALA MET                                              
SEQRES   1 B   52  VAL GLU CYS PRO LEU CYS MET GLU PRO LEU GLU ILE ASP          
SEQRES   2 B   52  ASP ILE ASN PHE PHE PRO CYS THR CYS GLY TYR GLN ILE          
SEQRES   3 B   52  CYS ARG PHE CYS TRP HIS ARG ILE ARG THR ASP GLU ASN          
SEQRES   4 B   52  GLY LEU CYS PRO ALA CYS ARG LYS PRO TYR PRO GLU ASP          
HET     ZN  B  79       1                                                       
HET     ZN  B  80       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   3   ZN    2(ZN 2+)                                                     
HELIX    1   1 LEU A    3  ASP A   16  1                                  14    
HELIX    2   2 LEU A   86  ARG A   90  5                                   5    
HELIX    3   3 THR A   98  CYS A  111  1                                  14    
HELIX    4   4 PRO A  121  ASP A  130  1                                  10    
HELIX    5   5 ASP A  130  TYR A  145  1                                  16    
HELIX    6   6 GLU B   22  ILE B   26  5                                   5    
HELIX    7   7 CYS B   38  ARG B   46  1                                   9    
SHEET    1  AA 3 HIS A  32  ILE A  37  0                                        
SHEET    2  AA 3 PHE A  50  HIS A  55 -1  O  PHE A  50   N  ILE A  37           
SHEET    3  AA 3 LYS A  66  PHE A  69 -1  O  LYS A  66   N  HIS A  55           
LINK         SG  CYS B  14                ZN    ZN B  79     1555   1555  2.47  
LINK         SG  CYS B  17                ZN    ZN B  79     1555   1555  2.46  
LINK         SG  CYS B  31                ZN    ZN B  80     1555   1555  2.36  
LINK         SG  CYS B  33                ZN    ZN B  80     1555   1555  2.51  
LINK         SG  CYS B  38                ZN    ZN B  79     1555   1555  2.35  
LINK         SG  CYS B  41                ZN    ZN B  79     1555   1555  2.45  
LINK         SG  CYS B  53                ZN    ZN B  80     1555   1555  2.52  
LINK         SG  CYS B  56                ZN    ZN B  80     1555   1555  2.41  
SITE     1 AC1  4 CYS B  14  CYS B  17  CYS B  38  CYS B  41                    
SITE     1 AC2  4 CYS B  31  CYS B  33  CYS B  53  CYS B  56                    
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