1KHQ | pdb_00001khq

ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX

• PDB DOI: https://doi.org/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.169 (Depositor) 
• R-Value Work: 
  0.147 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1111/j.1399-3011.2004.00181.x
• Primary Citation Related Structures: 
  1KHP, 1KHQ


• 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 23.96 kDa 
• Atom Count: 1,803 
• Modeled Residue Count: 216 
• Deposited Residue Count: 217 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptidic inhibitor	B [auth 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	B [auth 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 (Depositor) 
• R-Value Work:  0.147 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

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

• 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
• Version 1.4: 2023-08-16
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary