1KHP

Monoclinic form of papain/ZLFG-DAM covalent complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 

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:  

  • 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 ...

    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: 
    • 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 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
    • Structure of monoclinic papain at 1.60 Angstroms resolution.
      Pickersgill, R.W.,Harris, G.W.,Garman, E.
      (1992) ACTA CRYSTALLOGR.,SECT.B 48: 59
    • 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
    • Binding of chloromethyl ketone substrate analogues to crystalline papain.
      Drenth, J.,Kalk, K.H.,Swen, H.M.
      (1976) Biochemistry 15: 3731


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Papain
A
212Carica papayaMutation(s): 0 
EC: 3.4.22.2
Find proteins for P00784 (Carica papaya)
Go to UniProtKB:  P00784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptidic inhibitor
I
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
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: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.440α = 90.00
b = 48.930β = 112.42
c = 52.690γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other