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Database: PDB
Entry: 6KBO
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Original site: 6KBO 
HEADER    ANTIMICROBIAL PROTEIN                   26-JUN-19   6KBO              
TITLE     THREE-DIMENSIONAL LPS BOUND STRUCTURE OF VG16KRKP-KYE28.              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: VG16KRKP;                                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MOL_ID: 2;                                                           
COMPND   6 MOLECULE: HEPARIN COFACTOR 2;                                        
COMPND   7 CHAIN: B;                                                            
COMPND   8 FRAGMENT: HELIX-D;                                                   
COMPND   9 SYNONYM: KYE28;                                                      
COMPND  10 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: DENGUE VIRUS;                                   
SOURCE   4 ORGANISM_TAXID: 12637;                                               
SOURCE   5 MOL_ID: 2;                                                           
SOURCE   6 SYNTHETIC: YES;                                                      
SOURCE   7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   8 ORGANISM_COMMON: HUMAN;                                              
SOURCE   9 ORGANISM_TAXID: 9606                                                 
KEYWDS    ANTIMICROBIAL PEPTIDE, NUCLEAR MAGNETIC SPECTROSCOPY, PEPTIDE         
KEYWDS   2 SYNERGISM, LIPOPOLYSACCHARIDE (LPS), BACTERIAL MEMBRANE,             
KEYWDS   3 ANTIMICROBIAL PROTEIN                                                
EXPDTA    SOLUTION NMR                                                          
NUMMDL    15                                                                    
AUTHOR    H.ILYAS,A.BHUNIA                                                      
REVDAT   2   26-FEB-20 6KBO    1       JRNL                                     
REVDAT   1   14-AUG-19 6KBO    0                                                
JRNL        AUTH   H.ILYAS,J.KIM,D.LEE,M.MALMSTEN,A.BHUNIA                      
JRNL        TITL   STRUCTURAL INSIGHTS INTO THE COMBINATORIAL EFFECTS OF        
JRNL        TITL 2 ANTIMICROBIAL PEPTIDES REVEAL A ROLE OF AROMATIC-AROMATIC    
JRNL        TITL 3 INTERACTIONS IN ANTIBACTERIAL SYNERGISM.                     
JRNL        REF    J.BIOL.CHEM.                  V. 294 14615 2019              
JRNL        REFN                   ESSN 1083-351X                               
JRNL        PMID   31383740                                                     
JRNL        DOI    10.1074/JBC.RA119.009955                                     
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CYANA V2.1                                           
REMARK   3   AUTHORS     : GUNTERT, MUMENTHALER AND WUTHRICH                    
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6KBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-19.                  
REMARK 100 THE DEPOSITION ID IS D_1300012686.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 4.5                                
REMARK 210  IONIC STRENGTH                 : 0.6                                
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 0.3 MM 1H, NATURAL ABUNDANCE       
REMARK 210                                   VG16KRKP, 0.3 MM 1H, NATURAL       
REMARK 210                                   ABUNDANCE KYE28, 55.55 M 1H,       
REMARK 210                                   NATURAL ABUNDANCE WATER, 10 UM     
REMARK 210                                   1H, NATURAL ABUNDANCE              
REMARK 210                                   LIPOPOLYSACCHARIDE, 90% H2O/10%    
REMARK 210                                   D2O                                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-1H TOCSY; 2D 1H-1H NOESY     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 700 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE III                         
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : TOPSPIN 4.0.6, SPARKY 3.113,       
REMARK 210                                   CYANA V2.1                         
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 15                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 ALA A   2       65.32   -115.51                                   
REMARK 500  1 LYS A   8      -77.78    -58.73                                   
REMARK 500  1 PRO A  10       36.83    -69.78                                   
REMARK 500  1 TYR B   2      -55.20   -120.24                                   
REMARK 500  1 THR B  15      122.65    -34.05                                   
REMARK 500  1 HIS B  16       97.84    -48.13                                   
REMARK 500  1 ARG B  17      -50.42   -123.90                                   
REMARK 500  2 LYS A   8      -79.99    -65.86                                   
REMARK 500  2 PRO A  10       38.36    -69.66                                   
REMARK 500  2 ARG B  17       32.63    -96.63                                   
REMARK 500  3 LYS A   8      -76.24    -59.08                                   
REMARK 500  3 PRO A  10       37.10    -69.68                                   
REMARK 500  3 ASN B  22      -57.04   -123.94                                   
REMARK 500  4 ALA A   2       69.57   -115.43                                   
REMARK 500  4 LYS A   6      -54.35   -121.12                                   
REMARK 500  4 LYS A   8      -77.73    -59.48                                   
REMARK 500  4 PRO A  10       37.01    -69.74                                   
REMARK 500  4 ASN B   9      -60.17    -92.02                                   
REMARK 500  4 LYS B  13      -72.17   -120.29                                   
REMARK 500  4 HIS B  16     -120.22   -117.36                                   
REMARK 500  4 ASN B  22      -53.47   -121.89                                   
REMARK 500  5 LYS A   8      -75.25    -49.60                                   
REMARK 500  5 PRO A  10       36.59    -69.66                                   
REMARK 500  5 ARG B  12      -74.78    -76.02                                   
REMARK 500  5 LEU B  14      102.18    -44.59                                   
REMARK 500  5 THR B  15      -92.05   -100.20                                   
REMARK 500  5 HIS B  16      -83.37   -123.67                                   
REMARK 500  5 PHE B  19      -51.81   -121.93                                   
REMARK 500  5 ASN B  22      -55.20   -122.98                                   
REMARK 500  6 LYS A   8      -75.89    -49.03                                   
REMARK 500  6 PRO A  10       36.41    -69.78                                   
REMARK 500  6 LYS B  13      -74.43   -120.09                                   
REMARK 500  6 HIS B  16     -100.81   -122.29                                   
REMARK 500  6 ASN B  22      -57.76   -123.59                                   
REMARK 500  7 ALA A   2       65.12   -100.42                                   
REMARK 500  7 LYS A   6      -58.03   -120.89                                   
REMARK 500  7 LYS A   8      -75.95    -54.86                                   
REMARK 500  7 PRO A  10       37.30    -69.75                                   
REMARK 500  7 LYS B  13      -74.98   -105.33                                   
REMARK 500  7 LEU B  14     -122.12   -116.79                                   
REMARK 500  7 THR B  15      -90.90   -121.17                                   
REMARK 500  7 ARG B  17      -52.75   -120.87                                   
REMARK 500  7 ASN B  22      -53.40   -123.22                                   
REMARK 500  8 LYS A   8      -70.75    -50.29                                   
REMARK 500  8 PRO A  10       37.52    -69.76                                   
REMARK 500  8 ARG B  12      -83.43    -44.77                                   
REMARK 500  8 THR B  15      -94.45    -56.04                                   
REMARK 500  8 ARG B  17      -64.94   -121.68                                   
REMARK 500  8 LEU B  18        3.23    -68.86                                   
REMARK 500  8 ASN B  22      -61.77   -122.77                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      89 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 36265   RELATED DB: BMRB                                 
REMARK 900 THREE-DIMENSIONAL LPS BOUND STRUCTURE OF VG16KRKP-KYE28.             
DBREF  6KBO A    1    16  PDB    6KBO     6KBO             1     16             
DBREF  6KBO B    1    28  UNP    P05546   HEP2_HUMAN     192    219             
SEQRES   1 A   16  VAL ALA ARG GLY TRP LYS ARG LYS CYS PRO LEU PHE GLY          
SEQRES   2 A   16  LYS GLY GLY                                                  
SEQRES   1 B   28  LYS TYR GLU ILE THR THR ILE HIS ASN LEU PHE ARG LYS          
SEQRES   2 B   28  LEU THR HIS ARG LEU PHE ARG ARG ASN PHE GLY TYR THR          
SEQRES   3 B   28  LEU ARG                                                      
HELIX    1 AA1 TYR B    2  ILE B    7  1                                   6    
HELIX    2 AA2 ARG B   17  ASN B   22  1                                   6    
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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