PDB Short entry for 2D9Y
HEADER    SIGNALING PROTEIN                       13-DEC-05   2D9Y              
TITLE     SOLUTION STRUCTURE OF THE PH DOMAIN OF PEPP-3 FROM HUMAN              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN FAMILY A     
COMPND   3 MEMBER 6;                                                            
COMPND   4 CHAIN: A;                                                            
COMPND   5 FRAGMENT: PH DOMAIN;                                                 
COMPND   6 SYNONYM: PHOSPHOINOSITOL 3-PHOSPHATE-BINDING PROTEIN 3, PEPP-3;      
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 GENE: PLEKHA6;                                                       
SOURCE   6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   7 EXPRESSION_SYSTEM_PLASMID: P050711-08;                               
SOURCE   8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS                           
KEYWDS    PH DOMAIN, PEPP-3, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON   
KEYWDS   2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL         
KEYWDS   3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING PROTEIN              
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    H.LI,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL  
AUTHOR   2 GENOMICS/PROTEOMICS INITIATIVE (RSGI)                                
REVDAT   3   09-MAR-22 2D9Y    1       REMARK SEQADV                            
REVDAT   2   24-FEB-09 2D9Y    1       VERSN                                    
REVDAT   1   13-JUN-06 2D9Y    0                                                
JRNL        AUTH   H.LI,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA          
JRNL        TITL   SOLUTION STRUCTURE OF THE PH DOMAIN OF PEPP-3 FROM HUMAN     
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : XWINNMR 3.5, CYANA 2.0.17                            
REMARK   3   AUTHORS     : BRUKER (XWINNMR), GUNTERT, P. (CYANA)                
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2D9Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-05.                  
REMARK 100 THE DEPOSITION ID IS D_1000025169.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 296                                
REMARK 210  PH                             : 7.0                                
REMARK 210  IONIC STRENGTH                 : 120MM                              
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 1.14MM PH DOMAIN U-15N,13C; 20MM   
REMARK 210                                   D-TRIS-HCL(PH 7.0); 100MM NACL;    
REMARK 210                                   1MM D-DTT; 0.02% NAN3; 90% H2O,    
REMARK 210                                   10% D2O                            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_15N-SEPARATED_NOESY; 3D_13C     
REMARK 210                                   -SEPARATED_NOESY                   
REMARK 210  SPECTROMETER FIELD STRENGTH    : 900 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE 20030801, NMRVIEW 5.0.4,   
REMARK 210                                   KUJIRA 0.932, CYANA 2.0.17         
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS             
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : TARGET FUNCTION,STRUCTURES WITH    
REMARK 210                                   THE LEAST RESTRAINT VIOLATIONS     
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: 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 GLN A  20      145.22    -39.42                                   
REMARK 500  1 ALA A  21       98.24    -64.80                                   
REMARK 500  1 VAL A  25       74.05   -109.58                                   
REMARK 500  1 LYS A  26       35.55     37.24                                   
REMARK 500  1 LEU A  57       54.01   -117.27                                   
REMARK 500  1 VAL A  65      172.52    -58.38                                   
REMARK 500  1 SER A  72       58.67    -99.52                                   
REMARK 500  1 ALA A  82       40.85     71.26                                   
REMARK 500  1 VAL A  84      -74.92    -60.03                                   
REMARK 500  1 ILE A 101      -35.52    -38.72                                   
REMARK 500  1 PRO A 114     -179.62    -69.81                                   
REMARK 500  2 SER A  23      113.18   -174.49                                   
REMARK 500  2 VAL A  25      170.78    -49.50                                   
REMARK 500  2 LYS A  47      -38.52    -34.62                                   
REMARK 500  2 VAL A  65      176.00    -59.10                                   
REMARK 500  2 ALA A  82       73.78    -66.20                                   
REMARK 500  2 ILE A 101      -37.25    -39.83                                   
REMARK 500  3 ASN A   8      107.80    -36.28                                   
REMARK 500  3 ARG A  38       41.32     34.28                                   
REMARK 500  3 LYS A  47      -36.03    -35.56                                   
REMARK 500  3 LEU A  57       40.46   -106.03                                   
REMARK 500  3 VAL A  65      174.92    -53.74                                   
REMARK 500  3 ALA A  82       41.49     73.57                                   
REMARK 500  3 VAL A  84      -71.66    -52.64                                   
REMARK 500  4 GLN A  20      152.84    -38.57                                   
REMARK 500  4 SER A  23      100.37    -37.39                                   
REMARK 500  4 ARG A  38       38.63     39.81                                   
REMARK 500  4 GLU A  48       47.59     34.89                                   
REMARK 500  4 LEU A  57       57.05   -100.06                                   
REMARK 500  4 PRO A 114       94.61    -69.81                                   
REMARK 500  5 ARG A  38       32.35     34.62                                   
REMARK 500  5 GLU A  48       26.53     43.07                                   
REMARK 500  5 VAL A  65      176.34    -52.52                                   
REMARK 500  5 SER A  72       45.81    -83.44                                   
REMARK 500  5 HIS A  81       67.88   -112.22                                   
REMARK 500  5 ARG A  85      141.19   -174.31                                   
REMARK 500  5 ILE A 101      -35.59    -36.95                                   
REMARK 500  5 PRO A 114       85.23    -69.76                                   
REMARK 500  5 SER A 115      149.73    -39.81                                   
REMARK 500  6 SER A  23       49.34     71.62                                   
REMARK 500  6 VAL A  25      163.35    -49.91                                   
REMARK 500  6 ARG A  38       36.26     32.64                                   
REMARK 500  6 LYS A  47      -30.64    -36.86                                   
REMARK 500  6 GLU A  48       46.53     31.05                                   
REMARK 500  6 LEU A  57       46.04    -91.71                                   
REMARK 500  6 ALA A  63      142.75   -173.99                                   
REMARK 500  6 ALA A  64      132.05    -35.31                                   
REMARK 500  6 VAL A  65     -177.00    -54.02                                   
REMARK 500  6 SER A  72       43.74    -80.98                                   
REMARK 500  6 VAL A  84      -71.80    -60.70                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     202 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 650                                                                      
REMARK 650 HELIX                                                                
REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED                              
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: HSK002000946.1   RELATED DB: TARGETDB                    
DBREF  2D9Y A    8   111  UNP    Q9Y2H5   PLEA6_HUMAN     57    160             
SEQADV 2D9Y GLY A    1  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A    2  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A    3  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y GLY A    4  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A    5  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A    6  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y GLY A    7  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A  112  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y GLY A  113  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y PRO A  114  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A  115  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y SER A  116  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQADV 2D9Y GLY A  117  UNP  Q9Y2H5              CLONING ARTIFACT               
SEQRES   1 A  117  GLY SER SER GLY SER SER GLY ASN ALA PRO VAL THR LYS          
SEQRES   2 A  117  ALA GLY TRP LEU PHE LYS GLN ALA SER SER GLY VAL LYS          
SEQRES   3 A  117  GLN TRP ASN LYS ARG TRP PHE VAL LEU VAL ASP ARG CYS          
SEQRES   4 A  117  LEU PHE TYR TYR LYS ASP GLU LYS GLU GLU SER ILE LEU          
SEQRES   5 A  117  GLY SER ILE PRO LEU LEU SER PHE ARG VAL ALA ALA VAL          
SEQRES   6 A  117  GLN PRO SER ASP ASN ILE SER ARG LYS HIS THR PHE LYS          
SEQRES   7 A  117  ALA GLU HIS ALA GLY VAL ARG THR TYR PHE PHE SER ALA          
SEQRES   8 A  117  GLU SER PRO GLU GLU GLN GLU ALA TRP ILE GLN ALA MET          
SEQRES   9 A  117  GLY GLU ALA ALA ARG VAL GLN SER GLY PRO SER SER GLY          
HELIX    1   1 PRO A   94  ALA A  107  1                                  14    
SHEET    1   A 7 GLY A  53  PRO A  56  0                                        
SHEET    2   A 7 CYS A  39  TYR A  43 -1  N  LEU A  40   O  ILE A  55           
SHEET    3   A 7 TRP A  28  VAL A  36 -1  N  VAL A  36   O  CYS A  39           
SHEET    4   A 7 LYS A  13  GLN A  20 -1  N  LEU A  17   O  ARG A  31           
SHEET    5   A 7 THR A  86  SER A  90 -1  O  SER A  90   N  PHE A  18           
SHEET    6   A 7 THR A  76  GLU A  80 -1  N  ALA A  79   O  TYR A  87           
SHEET    7   A 7 ARG A  61  ALA A  64 -1  N  ALA A  63   O  LYS A  78           
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