Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.96 kDa 
• Atom Count: 1803 
• Residue Count: 216 
• Unique protein chains: 2

1KHQ

ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX

• DOI: 10.2210/pdb1KHQ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Carica papaya
• Mutation(s): No 


• Deposited: 2001-11-30 Released: 2003-09-09 
• Deposition Author(s): Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Jaskolski, M.

---

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 

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

• PubMed: 15357669 
• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain	A	212	Carica papaya	Mutation(s): 0  EC: 3.4.22.2
Find proteins for P00784 (Carica papaya) Explore P00784  Go to UniProtKB:  P00784

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptidic inhibitor	I	5	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000309	I	L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide	Peptide-like /  Inhibitor		--

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 = 42.89	α = 90
b = 96.74	β = 90
c = 49.88	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-30 
• Released Date: 2003-09-09 
Deposition Author(s): Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Jaskolski, M.

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