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Database: PDB
Entry: 2OTK
LinkDB: 2OTK
Original site: 2OTK 
HEADER    DE NOVO PROTEIN, PEPTIDE BINDING PROTEIN08-FEB-07   2OTK              
TITLE     STRUCTURE OF ALZHEIMER AB PEPTIDE IN COMPLEX WITH AN ENGINEERED       
TITLE    2 BINDING PROTEIN                                                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: AMYLOID BETA A4 PROTEIN;                                   
COMPND   3 CHAIN: C;                                                            
COMPND   4 FRAGMENT: RESIDUES 672-711;                                          
COMPND   5 SYNONYM: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A;            
COMPND   6 MOL_ID: 2;                                                           
COMPND   7 MOLECULE: ZAB3 AFFIBODY DIMER;                                       
COMPND   8 CHAIN: E, F;                                                         
COMPND   9 ENGINEERED: YES                                                      
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: ENGINEERED BINDING PROTEIN;                     
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    PROTEIN-PEPTIDE COMPLEX, BETA-HAIRPIN, INTERMOLECULAR BETA-SHEET, DE  
KEYWDS   2 NOVO PROTEIN, PEPTIDE BINDING PROTEIN                                
EXPDTA    SOLUTION NMR                                                          
NUMMDL    24                                                                    
AUTHOR    W.HOYER,T.HARD                                                        
REVDAT   4   04-DEC-19 2OTK    1       REMARK                                   
REVDAT   3   24-FEB-09 2OTK    1       VERSN                                    
REVDAT   2   22-APR-08 2OTK    1       JRNL                                     
REVDAT   1   12-FEB-08 2OTK    0                                                
JRNL        AUTH   W.HOYER,C.GRONWALL,A.JONSSON,S.STAHL,T.HARD                  
JRNL        TITL   STABILIZATION OF A BETA-HAIRPIN IN MONOMERIC ALZHEIMER'S     
JRNL        TITL 2 AMYLOID-BETA PEPTIDE INHIBITS AMYLOID FORMATION.             
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 105  5099 2008              
JRNL        REFN                   ISSN 0027-8424                               
JRNL        PMID   18375754                                                     
JRNL        DOI    10.1073/PNAS.0711731105                                      
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   C.GRONWALL,A.JONSSON,S.LINDSTROM,E.GUNNERIUSSON,S.STAHL,     
REMARK   1  AUTH 2 N.HERNE                                                      
REMARK   1  TITL   SELECTION AND CHARACTERIZATION OF AFFIBODY LIGANDS BINDING   
REMARK   1  TITL 2 TO ALZHEIMER AMYLOID BETA PEPTIDES                           
REMARK   1  REF    J.BIOTECHNOL.                 V. 128   162 2007              
REMARK   1  REFN                   ISSN 0168-1656                               
REMARK   1  PMID   17088007                                                     
REMARK   1  DOI    10.1016/J.JBIOTEC.2006.09.013                                
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : XPLOR-NIH 2.15.0                                     
REMARK   3   AUTHORS     : KUSZEWSKI ET AL                                      
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2OTK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-07.                  
REMARK 100 THE DEPOSITION ID IS D_1000041567.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298; 298                           
REMARK 210  PH                             : 7.2; 7.2                           
REMARK 210  IONIC STRENGTH                 : 20 MM SODIUM PHOPHATE; 20 MM       
REMARK 210                                   SODIUM PHOSPHATE                   
REMARK 210  PRESSURE                       : AMBIENT; AMBIENT                   
REMARK 210  SAMPLE CONTENTS                : 400 UM [U-100% 13C; U-100% 15N]    
REMARK 210                                   ABETA PEPTIDE, 400 UM ZAB3         
REMARK 210                                   DIMERS, 20 MM NA-PHOSPHATE         
REMARK 210                                   BUFFER, 90% H2O/10% D2O; 400 UM    
REMARK 210                                   ABETA PEPTIDE, 400 UM [U-100%      
REMARK 210                                   13C; U-100% 15N] ZAB3 DIMERS, 20   
REMARK 210                                   MM NA-PHOSPHATE BUFFER, 90% H2O/   
REMARK 210                                   10% D2O                            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY; 3D_15N     
REMARK 210                                   -SEPARATED_NOESY                   
REMARK 210  SPECTROMETER FIELD STRENGTH    : 900 MHZ; 800 MHZ                   
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : XPLOR-NIH 2.15.0, CCPNMR           
REMARK 210                                   ANALYSIS 1.10, NMRPIPE 2.3         
REMARK 210   METHOD USED                   : AB INITIO SIMULATED ANNEALING      
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 24                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH ACCEPTABLE         
REMARK 210                                   COVALENT GEOMETRY,STRUCTURES       
REMARK 210                                   WITH THE LEAST RESTRAINT           
REMARK 210                                   VIOLATIONS,STRUCTURES WITH THE     
REMARK 210                                   LOWEST ENERGY                      
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: INTERMOLECULAR NOES ASSIGNED BASED ON 3D F1 (13C,15N)        
REMARK 210  -FILTERED, F2 (13C OR 15N)-EDITED NOESY EXPERIMENTS                 
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: TRIMERIC                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, E, F                               
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-24                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     ASP C     1                                                      
REMARK 465     ALA C     2                                                      
REMARK 465     GLU C     3                                                      
REMARK 465     PHE C     4                                                      
REMARK 465     ARG C     5                                                      
REMARK 465     HIS C     6                                                      
REMARK 465     ASP C     7                                                      
REMARK 465     SER C     8                                                      
REMARK 465     GLY C     9                                                      
REMARK 465     TYR C    10                                                      
REMARK 465     GLU C    11                                                      
REMARK 465     VAL C    12                                                      
REMARK 465     HIS C    13                                                      
REMARK 465     HIS C    14                                                      
REMARK 465     GLN C    15                                                      
REMARK 465     GLY E   -10                                                      
REMARK 465     SER E    -9                                                      
REMARK 465     SER E    -8                                                      
REMARK 465     HIS E    -7                                                      
REMARK 465     HIS E    -6                                                      
REMARK 465     HIS E    -5                                                      
REMARK 465     HIS E    -4                                                      
REMARK 465     HIS E    -3                                                      
REMARK 465     HIS E    -2                                                      
REMARK 465     LEU E    -1                                                      
REMARK 465     GLN E     0                                                      
REMARK 465     VAL E     1                                                      
REMARK 465     ASP E     2                                                      
REMARK 465     ASN E     3                                                      
REMARK 465     LYS E     4                                                      
REMARK 465     PHE E     5                                                      
REMARK 465     ASN E     6                                                      
REMARK 465     LYS E     7                                                      
REMARK 465     GLU E     8                                                      
REMARK 465     MET E     9                                                      
REMARK 465     ALA E    10                                                      
REMARK 465     SER E    11                                                      
REMARK 465     ALA E    12                                                      
REMARK 465     GLY E    13                                                      
REMARK 465     PRO E    57                                                      
REMARK 465     LYS E    58                                                      
REMARK 465     VAL E    59                                                      
REMARK 465     ASP E    60                                                      
REMARK 465     GLY F   -10                                                      
REMARK 465     SER F    -9                                                      
REMARK 465     SER F    -8                                                      
REMARK 465     HIS F    -7                                                      
REMARK 465     HIS F    -6                                                      
REMARK 465     HIS F    -5                                                      
REMARK 465     HIS F    -4                                                      
REMARK 465     HIS F    -3                                                      
REMARK 465     HIS F    -2                                                      
REMARK 465     LEU F    -1                                                      
REMARK 465     GLN F     0                                                      
REMARK 465     VAL F     1                                                      
REMARK 465     ASP F     2                                                      
REMARK 465     ASN F     3                                                      
REMARK 465     LYS F     4                                                      
REMARK 465     PHE F     5                                                      
REMARK 465     ASN F     6                                                      
REMARK 465     LYS F     7                                                      
REMARK 465     GLU F     8                                                      
REMARK 465     MET F     9                                                      
REMARK 465     ALA F    10                                                      
REMARK 465     SER F    11                                                      
REMARK 465     ALA F    12                                                      
REMARK 465     GLY F    13                                                      
REMARK 465     PRO F    57                                                      
REMARK 465     LYS F    58                                                      
REMARK 465     VAL F    59                                                      
REMARK 465     ASP F    60                                                      
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                                                                      
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 SER C  26     -167.33     53.57                                   
REMARK 500  1 LEU F  19       72.56   -116.35                                   
REMARK 500  2 SER C  26       28.22     49.57                                   
REMARK 500  2 ASP E  37       95.83   -162.80                                   
REMARK 500  3 SER C  26       28.39     48.78                                   
REMARK 500  4 SER C  26      174.25    -56.72                                   
REMARK 500  5 LYS C  28      -23.51   -145.55                                   
REMARK 500  6 LEU F  19       72.26   -116.00                                   
REMARK 500  7 SER C  26       47.60    -78.96                                   
REMARK 500  7 LYS C  28       -1.31   -142.02                                   
REMARK 500  8 SER C  26       28.30     49.36                                   
REMARK 500  8 ASP E  37       75.27   -116.77                                   
REMARK 500  8 LEU F  19       72.35   -117.36                                   
REMARK 500  8 ASP F  37       84.47   -151.62                                   
REMARK 500  9 LEU F  19       78.07   -117.76                                   
REMARK 500 10 SER C  26       28.79     48.47                                   
REMARK 500 11 SER C  26       35.73     38.00                                   
REMARK 500 11 LEU F  19       72.11   -115.59                                   
REMARK 500 13 LEU F  19       71.06   -117.70                                   
REMARK 500 14 SER C  26       28.50     47.07                                   
REMARK 500 14 ASN C  27       -5.38     69.94                                   
REMARK 500 15 GLN E  55      -68.86    -91.00                                   
REMARK 500 16 SER C  26       28.22     48.20                                   
REMARK 500 17 SER C  26       43.49    -79.30                                   
REMARK 500 17 LEU F  19       72.91   -116.86                                   
REMARK 500 18 SER C  26       27.87     49.06                                   
REMARK 500 18 LEU E  19       60.07   -118.36                                   
REMARK 500 19 LEU F  19       74.38   -118.74                                   
REMARK 500 20 LEU F  19       72.12   -116.61                                   
REMARK 500 21 SER C  26       28.82     49.42                                   
REMARK 500 22 SER C  26     -169.83     54.18                                   
REMARK 500 24 LEU F  19       77.33   -118.49                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 FRAGMENTS E AND F IS A DIMER OF AN ENGINEERED BINDING                
REMARK 999 PROTEIN, DECRIBED IN THE GRONWALL ET AL (2007) J.                    
REMARK 999 BIOTECHNOL.                                                          
DBREF  2OTK C    1    40  UNP    P05067   A4_HUMAN       672    711             
DBREF  2OTK E  -10    60  PDB    2OTK     2OTK           -10     60             
DBREF  2OTK F  -10    60  PDB    2OTK     2OTK           -10     60             
SEQRES   1 C   40  ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS          
SEQRES   2 C   40  HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER          
SEQRES   3 C   40  ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL          
SEQRES   4 C   40  VAL                                                          
SEQRES   1 E   71  GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP          
SEQRES   2 E   71  ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU          
SEQRES   3 E   71  ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS          
SEQRES   4 E   71  ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER          
SEQRES   5 E   71  ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA          
SEQRES   6 E   71  GLN ALA PRO LYS VAL ASP                                      
SEQRES   1 F   71  GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP          
SEQRES   2 F   71  ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU          
SEQRES   3 F   71  ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS          
SEQRES   4 F   71  ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER          
SEQRES   5 F   71  ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA          
SEQRES   6 F   71  GLN ALA PRO LYS VAL ASP                                      
HELIX    1   1 SER C   26  LYS C   28  5                                   3    
HELIX    2   2 ASN E   23  ASP E   37  1                                  15    
HELIX    3   3 GLN E   40  GLN E   55  1                                  16    
HELIX    4   4 ASN F   23  ASP F   37  1                                  15    
HELIX    5   5 ASP F   37  GLN F   55  1                                  19    
SHEET    1   A 4 GLU E  15  TYR E  18  0                                        
SHEET    2   A 4 GLY C  29  VAL C  36 -1  N  LEU C  34   O  VAL E  17           
SHEET    3   A 4 LEU C  17  GLY C  25 -1  N  PHE C  20   O  GLY C  33           
SHEET    4   A 4 ILE F  16  LEU F  19 -1  O  LEU F  19   N  PHE C  19           
SSBOND   1 CYS E   28    CYS F   28                          1555   1555  2.02  
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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