PDBsum entry: 1khq

Hydrolase

PDB-id: 1khq

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

212 a.a. *

Ligands

LEU-PHE-GLM

Waters ×105

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1khq

Name:

Hydrolase

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

Biological unit:

Dimer (from PQS)

UniProt:

P00784 (PAPA1_CARPA)

Seq:

Struc:

Seq:

345 a.a.

Struc:

212 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.4.22.2   [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'.

Resolution:

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] [DOI: 10.1111/j.1399-3011.2004.00181.x]

Date:

30-Nov-01

Release date:

09-Sep-03

Related entries:

1pad
papain-acetyl-alanyl-alanyl-phenylalanyl-methylenylalanyl
derivative (/acaapack)
5pad
papain-benzyloxycarbonyl-glycyl-phenylalanyl-
methylenylglycyl derivative (/zgpgck)
6pad
papain-benzyloxycarbonyl-phenylalanyl-methylenylalanyl
derivative (/zpack)
9pap
... plus others (see Header records)

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Clefts

Surface

Key reference

DOI no: 10.1111/j.1399-3011.2004.00181.x

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.

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.