?

Promode Elastic




    Copyright ©  WASEDA Univ,Japan. All rights reserved.

    Header

    HEADER    TRANSFERASE                             16-DEC-03   1UU8              
    TITLE     STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1           
    COMPND    MOL_ID: 1;                                                            
    COMPND   2 MOLECULE: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1;             
    COMPND   3 CHAIN: A;                                                            
    COMPND   4 FRAGMENT: KINASE DOMAIN, RESIDUES 51-360;                            
    COMPND   5 SYNONYM: HPDK1;                                                      
    COMPND   6 EC: 2.7.1.37;                                                        
    COMPND   7 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: SPODOPTERA FRUGIPERDA;                            
    SOURCE   6 EXPRESSION_SYSTEM_TAXID: 7108;                                       
    SOURCE   7 EXPRESSION_SYSTEM_CELL_LINE: SF21;                                   
    SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;                          
    SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1;                                
    SOURCE  10 OTHER_DETAILS: BACULOVIRUS INFECTED                                  
    KEYWDS    PROTEIN KINASE, PKB, PDK1, INHIBITOR, LY333531, BISINDOLYL            
    KEYWDS   2 MALEIMIDE, BIM-1, DIABETES, CANCER, TRANSFERASE,                     
    KEYWDS   3 SERINE/THREONINE-PROTEIN KINASE                                      
    EXPDTA    X-RAY DIFFRACTION                                                     
    AUTHOR    D.KOMANDER,G.S.KULAR,A.W.SCHUTTELKOPF,M.DEAK,K.R.PRAKASH,             
    AUTHOR   2 J.BAIN,M.ELLIOT,M.GARRIDO-FRANCO,A.P.KOZIKOWSKI,D.R.ALESSI,          
    AUTHOR   3 D.M.F.VAN AALTEN                                                     
    REVDAT   2   24-FEB-09 1UU8    1       VERSN                                    
    REVDAT   1   04-MAR-04 1UU8    0                                                
    JRNL        AUTH   D.KOMANDER,G.S.KULAR,A.W.SCHUTTELKOPF,M.DEAK,                
    JRNL        AUTH 2 K.R.PRAKASH,J.BAIN,M.ELLIOT,M.GARRIDO-FRANCO,                
    JRNL        AUTH 3 A.P.KOZIKOWSKI,D.R.ALESSI,D.M.F.VAN AALTEN                   
    JRNL        TITL   INTERACTIONS OF LY333531 AND OTHER BISINDOLYL                
    JRNL        TITL 2 MALEIMIDE INHIBITORS WITH PDK1                               
    JRNL        REF    STRUCTURE                     V.  12   215 2004              
    JRNL        REFN                   ISSN 0969-2126                               
    JRNL        PMID   14962382                                                     
    JRNL        DOI    10.1016/J.STR.2004.01.005                                    
    REMARK   2                                                                      
    REMARK   2 RESOLUTION.    2.5  ANGSTROMS.                                       
    REMARK   3                                                                      
    REMARK   3 REFINEMENT.                                                          
    REMARK   3   PROGRAM     : REFMAC                                               
    REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
    REMARK   3                                                                      
    REMARK   3  DATA USED IN REFINEMENT.                                            
    REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50                           
    REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 24.32                          
    REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.0                            
    REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.9                           
    REMARK   3   NUMBER OF REFLECTIONS             : 13551                          
    REMARK   3                                                                      
    REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
    REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
    REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
    REMARK   3   R VALUE     (WORKING + TEST SET) : 0.17642                         
    REMARK   3   R VALUE            (WORKING SET) : 0.198                           
    REMARK   3   FREE R VALUE                     : 0.258                           
    REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.0                             
    REMARK   3   FREE R VALUE TEST SET COUNT      : 547                             
    REMARK   3                                                                      
    REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
    REMARK   3   PROTEIN ATOMS            : 2213                                    
    REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
    REMARK   3   HETEROGEN ATOMS          : 98                                      
    REMARK   3   SOLVENT ATOMS            : 47                                      
    REMARK   3                                                                      
    REMARK   3  B VALUES.                                                           
    REMARK   3   FROM WILSON PLOT           (A**2) : 50.9                           
    REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 43.1                           
    REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
    REMARK   3    B11 (A**2) : 3.19                                                 
    REMARK   3    B22 (A**2) : 3.19                                                 
    REMARK   3    B33 (A**2) : -6.37                                                
    REMARK   3    B12 (A**2) : -0.59                                                
    REMARK   3    B13 (A**2) : 0.00                                                 
    REMARK   3    B23 (A**2) : 0.00                                                 
    REMARK   3                                                                      
    REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
    REMARK   3   ESU BASED ON R VALUE                            (A): 0.159         
    REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.152         
    REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.122         
    REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.062         
    REMARK   3                                                                      
    REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
    REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA               
    REMARK   3    BOND LENGTH                     (A) : NULL  ; NULL                
    REMARK   3    ANGLE DISTANCE                  (A) : NULL  ; NULL                
    REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : NULL  ; NULL                
    REMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL                
    REMARK   3                                                                      
    REMARK   3   PLANE RESTRAINT                  (A) : NULL  ; NULL                
    REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : NULL  ; NULL                
    REMARK   3                                                                      
    REMARK   3   NON-BONDED CONTACT RESTRAINTS.                                     
    REMARK   3    SINGLE TORSION                  (A) : NULL  ; NULL                
    REMARK   3    MULTIPLE TORSION                (A) : NULL  ; NULL                
    REMARK   3    H-BOND (X...Y)                  (A) : NULL  ; NULL                
    REMARK   3    H-BOND (X-H...Y)                (A) : NULL  ; NULL                
    REMARK   3                                                                      
    REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.                           
    REMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL                
    REMARK   3    PLANAR                    (DEGREES) : NULL  ; NULL                
    REMARK   3    STAGGERED                 (DEGREES) : NULL  ; NULL                
    REMARK   3    TRANSVERSE                (DEGREES) : NULL  ; NULL                
    REMARK   3                                                                      
    REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
    REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
    REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
    REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
    REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
    REMARK   3                                                                      
    REMARK   3  OTHER REFINEMENT REMARKS: SOME SIDECHAINS REFINED WITH              
    REMARK   3  OCCUPANCY = 0.00 DUE TO DISORDER. SOME RESIDUES MODELED AS          
    REMARK   3  ALANINE DUE TO DISORDER.                                            
    REMARK   4                                                                      
    REMARK   4 1UU8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
    REMARK 100                                                                      
    REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-03.                  
    REMARK 100 THE PDBE ID CODE IS EBI-14228.                                       
    REMARK 200                                                                      
    REMARK 200 EXPERIMENTAL DETAILS                                                 
    REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
    REMARK 200  DATE OF DATA COLLECTION        : 15-FEB-03                          
    REMARK 200  TEMPERATURE           (KELVIN) : 100.0                              
    REMARK 200  PH                             : 7.50                               
    REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
    REMARK 200                                                                      
    REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
    REMARK 200  RADIATION SOURCE               : ESRF                               
    REMARK 200  BEAMLINE                       : ID14-1                             
    REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
    REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
    REMARK 200  WAVELENGTH OR RANGE        (A) : 0.934                              
    REMARK 200  MONOCHROMATOR                  : NULL                               
    REMARK 200  OPTICS                         : NULL                               
    REMARK 200                                                                      
    REMARK 200  DETECTOR TYPE                  : CCD                                
    REMARK 200  DETECTOR MANUFACTURER          : ADSC                               
    REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
    REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
    REMARK 200                                                                      
    REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 13556                              
    REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.500                              
    REMARK 200  RESOLUTION RANGE LOW       (A) : 25.000                             
    REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
    REMARK 200                                                                      
    REMARK 200 OVERALL.                                                             
    REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.6                               
    REMARK 200  DATA REDUNDANCY                : 3.000                              
    REMARK 200  R MERGE                    (I) : 0.08900                            
    REMARK 200  R SYM                      (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 9.8000                             
    REMARK 200                                                                      
    REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
    REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50                     
    REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.59                     
    REMARK 200  COMPLETENESS FOR SHELL     (%) : 75.6                               
    REMARK 200  DATA REDUNDANCY IN SHELL       : 2.60                               
    REMARK 200  R MERGE FOR SHELL          (I) : 0.54900                            
    REMARK 200  R SYM FOR SHELL            (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.000                              
    REMARK 200                                                                      
    REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
    REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
    REMARK 200 SOFTWARE USED: AMORE                                                 
    REMARK 200 STARTING MODEL: PDB ENTRY 1H1W                                       
    REMARK 200                                                                      
    REMARK 200 REMARK: NULL                                                         
    REMARK 280                                                                      
    REMARK 280 CRYSTAL                                                              
    REMARK 280 SOLVENT CONTENT, VS  (%): 58                                         
    REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3                        
    REMARK 280                                                                      
    REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 M AMMONIUM SULPHATE,                 
    REMARK 280  0.1 M TRIS-HCL PH 7.50                                              
    REMARK 290                                                                      
    REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
    REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1                         
    REMARK 290                                                                      
    REMARK 290      SYMOP   SYMMETRY                                                
    REMARK 290     NNNMMM   OPERATOR                                                
    REMARK 290       1555   X,Y,Z                                                   
    REMARK 290       2555   -Y,X-Y,Z+2/3                                            
    REMARK 290       3555   -X+Y,-X,Z+1/3                                           
    REMARK 290       4555   Y,X,-Z                                                  
    REMARK 290       5555   X-Y,-Y,-Z+1/3                                           
    REMARK 290       6555   -X,-X+Y,-Z+2/3                                          
    REMARK 290                                                                      
    REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
    REMARK 290           MMM -> TRANSLATION VECTOR                                  
    REMARK 290                                                                      
    REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
    REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
    REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
    REMARK 290 RELATED MOLECULES.                                                   
    REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
    REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
    REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
    REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000            
    REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
    REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       32.01067            
    REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
    REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
    REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       16.00533            
    REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000            
    REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000            
    REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
    REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000            
    REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000            
    REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       16.00533            
    REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000            
    REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000            
    REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       32.01067            
    REMARK 290                                                                      
    REMARK 290 REMARK: NULL                                                         
    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 GENERATING THE BIOMOLECULE                                           
    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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
    REMARK 350 SOFTWARE USED: PQS                                                   
    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 375                                                                      
    REMARK 375 SPECIAL POSITION                                                     
    REMARK 375      HOH A2035  LIES ON A SPECIAL POSITION.                          
    REMARK 465                                                                      
    REMARK 465 MISSING RESIDUES                                                     
    REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
    REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
    REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
    REMARK 465                                                                      
    REMARK 465   M RES C SSSEQI                                                     
    REMARK 465     MET A    51                                                      
    REMARK 465     ASP A    52                                                      
    REMARK 465     GLY A    53                                                      
    REMARK 465     THR A    54                                                      
    REMARK 465     ALA A    55                                                      
    REMARK 465     ALA A    56                                                      
    REMARK 465     GLU A    57                                                      
    REMARK 465     PRO A    58                                                      
    REMARK 465     ARG A    59                                                      
    REMARK 465     PRO A    60                                                      
    REMARK 465     GLY A    61                                                      
    REMARK 465     ALA A    62                                                      
    REMARK 465     GLY A    63                                                      
    REMARK 465     SER A    64                                                      
    REMARK 465     LEU A    65                                                      
    REMARK 465     GLN A    66                                                      
    REMARK 465     HIS A    67                                                      
    REMARK 465     ALA A    68                                                      
    REMARK 465     GLN A    69                                                      
    REMARK 465     PRO A    70                                                      
    REMARK 465     PRO A    71                                                      
    REMARK 465     PRO A   232                                                      
    REMARK 465     GLU A   233                                                      
    REMARK 465     SER A   234                                                      
    REMARK 465     LYS A   235                                                      
    REMARK 465     GLN A   236                                                      
    REMARK 465     ALA A   237                                                      
    REMARK 465     ARG A   238                                                      
    REMARK 465     ALA A   239                                                      
    REMARK 465     THR A   359                                                      
    REMARK 465     ALA A   360                                                      
    REMARK 470                                                                      
    REMARK 470 MISSING ATOM                                                         
    REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
    REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
    REMARK 470 I=INSERTION CODE):                                                   
    REMARK 470   M RES CSSEQI  ATOMS                                                
    REMARK 470     GLN A  73    CG   CD   OE1  NE2                                  
    REMARK 470     ARG A  75    CG   CD   NE   CZ   NH1  NH2                        
    REMARK 470     ARG A 116    CG   CD   NE   CZ   NH1  NH2                        
    REMARK 470     LYS A 120    CG   CD   CE   NZ                                   
    REMARK 470     LYS A 169    CG   CD   CE   NZ                                   
    REMARK 470     GLU A 215    CG   CD   OE1  OE2                                  
    REMARK 470     LYS A 228    CG   CD   CE   NZ                                   
    REMARK 470     LYS A 257    CG   CD   CE   NZ                                   
    REMARK 470     GLU A 303    CG   CD   OE1  OE2                                  
    REMARK 470     LYS A 304    CG   CD   CE   NZ                                   
    REMARK 470     LYS A 323    CG   CD   CE   NZ                                   
    REMARK 470     GLU A 328    CG   CD   OE1  OE2                                  
    REMARK 470     LYS A 357    CG   CD   CE   NZ                                   
    REMARK 470     LEU A 358    CA   C    O    CB   CG   CD1  CD2                   
    REMARK 480                                                                      
    REMARK 480 ZERO OCCUPANCY ATOM                                                  
    REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO                  
    REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS                
    REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER;                                
    REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
    REMARK 480 I=INSERTION CODE):                                                   
    REMARK 480   M RES CSSEQI  ATOMS                                                
    REMARK 480     ARG A  78    NE   CZ  NH1  NH2                                   
    REMARK 480     LYS A 163    CD   CE   NZ                                        
    REMARK 480     LYS A 173    CD   CE   NZ                                        
    REMARK 480     LYS A 199    CE   NZ                                             
    REMARK 480     GLU A 256    CD  OE1  OE2                                        
    REMARK 480     SER A 258    OG                                                  
    REMARK 480     GLU A 343    CD  OE1  OE2                                        
    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 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    ASP A 151     -159.21   -117.92                                   
    REMARK 500    ASP A 205       46.73   -165.17                                   
    REMARK 500    ASP A 223       71.98     63.01                                   
    REMARK 500    LYS A 257       66.75     60.75                                   
    REMARK 500    SER A 258      122.07    179.61                                   
    REMARK 500    ASN A 349       51.05   -164.33                                   
    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    TYR A 185         0.06    SIDE CHAIN                              
    REMARK 500                                                                      
    REMARK 500 REMARK: NULL                                                         
    REMARK 525                                                                      
    REMARK 525 SOLVENT                                                              
    REMARK 525                                                                      
    REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
    REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
    REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
    REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
    REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
    REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
    REMARK 525 NUMBER; I=INSERTION CODE):                                           
    REMARK 800                                                                      
    REMARK 800 SITE                                                                 
    REMARK 800 SITE_IDENTIFIER: AC1                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1365                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC2                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1366                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC3                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1367                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC4                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BI1 A1368                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC5                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1358                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC6                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1359                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC7                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1360                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC8                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1361                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: AC9                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1362                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: BC1                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1363                 
    REMARK 800                                                                      
    REMARK 800 SITE_IDENTIFIER: BC2                                                 
    REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
    REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1364                 
    REMARK 900                                                                      
    REMARK 900 RELATED ENTRIES                                                      
    REMARK 900 RELATED ID: 1H1W   RELATED DB: PDB                                   
    REMARK 900  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE                            
    REMARK 900  HUMAN PDK1 CATALYTIC DOMAIN                                         
    REMARK 900 RELATED ID: 1OKY   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH STAUROSPORINE                                          
    REMARK 900 RELATED ID: 1OKZ   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH UCN-01                                                 
    REMARK 900 RELATED ID: 1UU3   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH LY333531                                               
    REMARK 900 RELATED ID: 1UU7   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH BIM-2                                                  
    REMARK 900 RELATED ID: 1UU9   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH BIM-3                                                  
    REMARK 900 RELATED ID: 1UVR   RELATED DB: PDB                                   
    REMARK 900  STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN                            
    REMARK 900  COMPLEX WITH BIM-8                                                  
    DBREF  1UU8 A   51   360  UNP    O15530   PDPK_HUMAN      51    360             
    SEQRES   1 A  310  MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY ALA GLY          
    SEQRES   2 A  310  SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG LYS          
    SEQRES   3 A  310  LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU GLY          
    SEQRES   4 A  310  GLU GLY SER PHE SER THR VAL VAL LEU ALA ARG GLU LEU          
    SEQRES   5 A  310  ALA THR SER ARG GLU TYR ALA ILE LYS ILE LEU GLU LYS          
    SEQRES   6 A  310  ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR VAL THR          
    SEQRES   7 A  310  ARG GLU ARG ASP VAL MET SER ARG LEU ASP HIS PRO PHE          
    SEQRES   8 A  310  PHE VAL LYS LEU TYR PHE THR PHE GLN ASP ASP GLU LYS          
    SEQRES   9 A  310  LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU LEU          
    SEQRES  10 A  310  LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU THR          
    SEQRES  11 A  310  CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA LEU          
    SEQRES  12 A  310  GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP LEU          
    SEQRES  13 A  310  LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS ILE          
    SEQRES  14 A  310  GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER PRO          
    SEQRES  15 A  310  GLU SER LYS GLN ALA ARG ALA ASN SEP PHE VAL GLY THR          
    SEQRES  16 A  310  ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SER          
    SEQRES  17 A  310  ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS ILE          
    SEQRES  18 A  310  ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG ALA          
    SEQRES  19 A  310  GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE LYS LEU          
    SEQRES  20 A  310  GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA ARG          
    SEQRES  21 A  310  ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR LYS          
    SEQRES  22 A  310  ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO LEU          
    SEQRES  23 A  310  LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU ASN          
    SEQRES  24 A  310  LEU HIS GLN GLN THR PRO PRO LYS LEU THR ALA                  
    MODRES 1UU8 SEP A  241  SER  PHOSPHOSERINE                                      
    HET    SEP  A 241      10                                                       
    HET    SO4  A1365       5                                                       
    HET    SO4  A1366       5                                                       
    HET    SO4  A1367       5                                                       
    HET    BI1  A1368      31                                                       
    HET    GOL  A1358       6                                                       
    HET    GOL  A1359       6                                                       
    HET    GOL  A1360       6                                                       
    HET    GOL  A1361       6                                                       
    HET    GOL  A1362       6                                                       
    HET    GOL  A1363       6                                                       
    HET    GOL  A1364       6                                                       
    HETNAM     SEP PHOSPHOSERINE                                                    
    HETNAM     SO4 SULFATE ION                                                      
    HETNAM     BI1 3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}                    
    HETNAM   2 BI1  -4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE                         
    HETNAM     GOL GLYCEROL                                                         
    HETSYN     BI1 RBT205 INHIBITOR                                                 
    HETSYN     SEP PHOSPHONOSERINE                                                  
    FORMUL   1  SEP    C3 H8 N O6 P                                                 
    FORMUL   2  SO4    3(O4 S 2-)                                                   
    FORMUL   5  BI1    C25 H24 N4 O2                                                
    FORMUL   6  GOL    7(C3 H8 O3)                                                  
    FORMUL  13  HOH   *47(H2 O1)                                                    
    HELIX    1   1 ARG A   78  GLU A   80  5                                   3    
    HELIX    2   2 LYS A  115  GLU A  121  1                                   7    
    HELIX    3   3 LYS A  123  SER A  135  1                                  13    
    HELIX    4   4 GLU A  166  GLY A  175  1                                  10    
    HELIX    5   5 ASP A  178  LYS A  199  1                                  22    
    HELIX    6   6 THR A  245  VAL A  249  5                                   5    
    HELIX    7   7 CYS A  260  GLY A  278  1                                  19    
    HELIX    8   8 ASN A  286  LEU A  297  1                                  12    
    HELIX    9   9 PHE A  306  LEU A  317  1                                  12    
    HELIX   10  10 ASP A  320  ARG A  324  5                                   5    
    HELIX   11  11 CYS A  327  GLU A  331  5                                   5    
    HELIX   12  12 GLY A  332  HIS A  339  1                                   8    
    HELIX   13  13 PRO A  340  GLU A  343  5                                   4    
    HELIX   14  14 THR A  346  GLN A  353  5                                   8    
    SHEET    1  AA 5 PHE A  82  GLU A  90  0                                        
    SHEET    2  AA 5 SER A  94  GLU A 101 -1  O  VAL A  96   N  LEU A  88           
    SHEET    3  AA 5 GLU A 107  GLU A 114 -1  O  TYR A 108   N  ALA A  99           
    SHEET    4  AA 5 LYS A 154  LEU A 159 -1  O  LEU A 155   N  LEU A 113           
    SHEET    5  AA 5 LEU A 145  GLN A 150 -1  N  TYR A 146   O  GLY A 158           
    SHEET    1  AB 2 ILE A 201  ILE A 202  0                                        
    SHEET    2  AB 2 LYS A 228  VAL A 229 -1  O  LYS A 228   N  ILE A 202           
    SHEET    1  AC 2 ILE A 211  LEU A 213  0                                        
    SHEET    2  AC 2 ILE A 219  ILE A 221 -1  O  GLN A 220   N  LEU A 212           
    LINK         C   ASN A 240                 N   SEP A 241     1555   1555  1.33  
    LINK         C   SEP A 241                 N   PHE A 242     1555   1555  1.33  
    SITE     1 AC1  4 TYR A 146  SER A 160  GLN A 220  GOL A1363                    
    SITE     1 AC2  4 ARG A 106  PRO A 140  HIS A 351  GOL A1363                    
    SITE     1 AC3  5 GLY A  91  SER A  92  PHE A  93  SER A  94                    
    SITE     2 AC3  5 GOL A1360                                                     
    SITE     1 AC4 14 LEU A  88  GLY A  89  ALA A 109  VAL A 143                    
    SITE     2 AC4 14 LEU A 159  SER A 160  TYR A 161  ALA A 162                    
    SITE     3 AC4 14 GLU A 166  GLU A 209  LEU A 212  THR A 222                    
    SITE     4 AC4 14 ASP A 223  GOL A1360                                          
    SITE     1 AC5  7 LYS A  76  ARG A 131  THR A 148  PHE A 149                    
    SITE     2 AC5  7 GLN A 150  LEU A 155  HOH A2010                               
    SITE     1 AC6  6 PRO A  79  LYS A 154  TYR A 156  GLU A 328                    
    SITE     2 AC6  6 GLU A 331  GLY A 332                                          
    SITE     1 AC7  5 SER A  94  VAL A  96  LYS A 111  SO4 A1367                    
    SITE     2 AC7  5 BI1 A1368                                                     
    SITE     1 AC8  5 LEU A 297  TYR A 299  PHE A 301  ARG A 310                    
    SITE     2 AC8  5 HOH A2034                                                     
    SITE     1 AC9  5 LYS A  83  PHE A  84  GLU A 194  GLY A 334                    
    SITE     2 AC9  5 LYS A 337                                                     
    SITE     1 BC1  7 ARG A 106  GLU A 107  TYR A 108  SER A 160                    
    SITE     2 BC1  7 TYR A 161  SO4 A1365  SO4 A1366                               
    SITE     1 BC2  9 ALA A 103  THR A 104  SER A 105  HIS A 139                    
    SITE     2 BC2  9 SER A 191  TRP A 347  ASN A 349  LEU A 350                    
    SITE     3 BC2  9 HIS A 351                                                     
    CRYST1  122.397  122.397   48.016  90.00  90.00 120.00 P 32 2 1      6          
    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      0.008170  0.004717  0.000000        0.00000                         
    SCALE2      0.000000  0.009434  0.000000        0.00000                         
    SCALE3      0.000000  0.000000  0.020826        0.00000                         

    3D molecular view of vibration

    Displacement vectors
    Display
    Animation
    Display

    Still image of displacement vectors and GIF animation


    Mode 1

    Time-average properties and properties of the 10 lowest-frequency modes

    Fluctuation of atoms:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of dihedral angles:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of atomsFluctuation of dihedral angles

    Correlations between fluctuations of atoms

    Mode 1
    Correlations between fluctuations of atoms - Mode 1
    Time Average
    Time Average
    Distance map
    Distance map

    Calculation note

    PDB file name : pdb1uu8.ent

    Chains and HETATMs selected: 
      ATOM        A

    The following atoms are removed from PDB data on concern that they may have 
    abnormally large fluctuations, because they interact with few atoms.
      ATOM     94  CG  LYS A  83      35.668  75.125  44.280  1.00 44.13           C  
      ATOM     95  CD  LYS A  83      37.051  75.355  44.875  1.00 47.41           C  
      ATOM     96  CE  LYS A  83      37.193  76.721  45.471  1.00 51.16           C  
      ATOM     97  NZ  LYS A  83      36.974  77.770  44.426  1.00 56.13           N  
      ATOM   2221  N   LEU A 358      39.100  95.673  18.060  1.00 62.78           N  

    = Normal mode analysis calculation =

    No. of modes used in the calculation : All modes.

    Parameters of potential energies:
      1-4 and 1-5 non-bonded interactions: E(d) = A*exp(-d(PDB)**2/B**2)(d-d(PDB))**2.
      Loop-closing potential:              E(d) = A*(d-d(PDB))**2.
        for a disulfide bond and one of the bonds in the DNA and RNA sugar ring.
      where d and d(PDB) are distances between atoms in calculation and in PDB data, 
      respectively.

      Interaction type   A       B      Cutoff distance (A)
        1-4             1.00    5.00      100.00
        1-5             1.00    5.00      100.00
        Loop-closing  100.00

    Temperature adjustment by magnitude of fluctuation:
      Set to mean displacements of atoms       0.500 A

    Animation
      No. of frames: 11
      Mean displacements (A):    0.50

    Displacement vector
      Mean length of vectors (A):    3.00