PDBsum entry 1khq

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Hydrolase/hydrolase inhibitor PDB id
Jmol PyMol
Protein chain
212 a.a. *
Waters ×105
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Orthorhombic form of papain/zlfg-dam covalent complex
Structure: Papain. Chain: a. Fragment: papain, residues 134-345. Synonym: papaya proteinase i, ppi. Peptidic inhibitor. Chain: i. Engineered: yes
Source: Carica papaya. Papaya. Organism_taxid: 3649. Synthetic: yes
Biol. unit: Dimer (from PQS)
1.60Å     R-factor:   0.149     R-free:   0.169
Authors: R.Janowski,M.Kozak,E.Jankowska,Z.Grzonka,M.Jaskolski
Key ref: R.Janowski et al. (2004). Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor. J Pept Res, 64, 141-150. PubMed id: 15357669
30-Nov-01     Release date:   09-Sep-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00784  (PAPA1_CARPA) -  Papain
345 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Papain.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, with preference for a residue bearing a large hydrophobic sidechain at the P2 position. Does not accept Val at P1'.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     cysteine-type peptidase activity     1 term  


J Pept Res 64:141-150 (2004)
PubMed id: 15357669  
Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor.
R.Janowski, M.Kozak, E.Jankowska, Z.Grzonka, M.Jaskólski.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19857201 M.Klimacek, and B.Nidetzky (2010).
The oxyanion hole of Pseudomonas fluorescens mannitol 2-dehydrogenase: a novel structural motif for electrostatic stabilization in alcohol dehydrogenase active sites.
  Biochem J, 425, 455-463.  
19143838 I.Redzynia, A.Ljunggren, A.Bujacz, M.Abrahamson, M.Jaskolski, and G.Bujacz (2009).
Crystal structure of the parasite inhibitor chagasin in complex with papain allows identification of structural requirements for broad reactivity and specificity determinants for target proteases.
  FEBS J, 276, 793-806.
PDB code: 3e1z
19430116 T.K.Nandi, H.R.Bairagya, B.P.Mukhopadhyay, K.Sekar, D.Sukul, and A.K.Bera (2009).
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease.
  J Biosci, 34, 27-34.  
17452780 J.A.Gavira, L.A.González-Ramírez, M.C.Oliver-Salvador, M.Soriano-García, and J.M.García-Ruiz (2007).
Structure of the mexicain-E-64 complex and comparison with other cysteine proteases of the papain family.
  Acta Crystallogr D Biol Crystallogr, 63, 555-563.  
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