1KHQ

ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor

Janowski, R.Kozak, M.Jankowska, E.Grzonka, Z.Jaskolski, M.

(2004) J Pept Res 64: 141-150

  • DOI: 10.1111/j.1399-3011.2004.00181.x
  • Primary Citation of Related Structures:  
    1KHQ, 1KHP

  • PubMed Abstract: 
  • The three-dimensional structure of two polymorphs of a ZLFG-CH2-papain covalent complex has been determined by X-ray crystallography. The structures indicate that: (i) the methylene carbon atom of the inhibitor is covalently bound to the Sgamma atom of C ...

    The three-dimensional structure of two polymorphs of a ZLFG-CH2-papain covalent complex has been determined by X-ray crystallography. The structures indicate that: (i) the methylene carbon atom of the inhibitor is covalently bound to the Sgamma atom of Cys25 of papain; (ii) the hydrophobic S2 pocket formed by Pro68, Val133, Val157, and Asp158 is occupied by the inhibitor's phenylalanyl P2 side chain; (iii) extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme. Comparison with similar structures suggests that in covalent complexes preservation of main chain-main chain interactions between the enzyme and the inhibitor may have higher priority than the P-S interactions.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of a new crystal form of papain from Carica papaya.
      Kozak, M., Kozian, E., Grzonka, Z., Jaskolski, M.
      (1997) Acta Biochim Pol 44: 601
    • Structural studies of cysteine proteases and their inhibitors
      Grzonka, Z., Jankowska, E., Wieczerzak, E., Kasprzykowski, F., Lankiewicz, L., Wiczk, W., Drabik, P., Ciarkowski, J., Janowski, R., Kozak, M., Jaskolski, M., Grubb, A.
      (2001) Acta Biochim Pol 48: 1
    • Binding of chloromethyl ketone substrate analogues to crystalline papain.
      Drenth, J., Kalk, K.H., Swen, H.M.
      (1976) Biochemistry 15: 3731
    • Structure of monoclinic papain at 1.60 Angstroms resolution
      Pickersgill, R.W., Harris, G.W., Garman, E.
      (1992) Acta Crystallogr B 48: 59
    • Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
      Czaplewski, C., Grzonka, Z., Jaskolski, M., Kasprzykowski, F., Kozak, M., Politowska, E., Ciarkowski, J.
      (1999) Biochim Biophys Acta 1431: 290

    Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Papain A212Carica papayaMutation(s): 0 
EC: 3.4.22.2
Find proteins for P00784 (Carica papaya)
Explore P00784 
Go to UniProtKB:  P00784
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptidic inhibitor I5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000309
Query on PRD_000309
IL-leucyl-N-(2-oxopropyl)-L-phenylalaninamidePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.89α = 90
b = 96.74β = 90
c = 49.88γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other