PDBsum entry 1khq

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Hydrolase/hydrolase inhibitor PDB id
Protein chain
212 a.a. *
Waters ×105
* Residue conservation analysis

References listed in PDB file
Key reference
Title Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor.
Authors R.Janowski, M.Kozak, E.Jankowska, Z.Grzonka, M.Jaskólski.
Ref. J Pept Res, 2004, 64, 141-150. [DOI no: 10.1111/j.1399-3011.2004.00181.x]
PubMed id 15357669
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.
Secondary reference #1
Title Crystallization and preliminary crystallographic studies of a new crystal form of papain from carica papaya.
Authors M.Kozak, E.Kozian, Z.Grzonka, M.Jaskólski.
Ref. Acta Biochim Pol, 1997, 44, 601-605.
PubMed id 9511969
Secondary reference #2
Title Structural studies of cysteine proteases and their inhibitors.
Authors Z.Grzonka, E.Jankowska, F.Kasprzykowski, R.Kasprzykowska, L.Lankiewicz, W.Wiczk, E.Wieczerzak, J.Ciarkowski, P.Drabik, R.Janowski, M.Kozak, M.Jaskólski, A.Grubb.
Ref. Acta Biochim Pol, 2001, 48, 1.
PubMed id 11440158
Secondary reference #3
Title Binding of chloromethyl ketone substrate analogues to crystalline papain.
Authors J.Drenth, K.H.Kalk, H.M.Swen.
Ref. Biochemistry, 1976, 15, 3731-3738. [DOI no: 10.1021/bi00662a014]
PubMed id 952885
Full text Abstract
Secondary reference #4
Title Structure of monoclinic papain at 1.60 angstroms resolution
Authors R.W.Pickersgill, G.W.Harris, E.Garman.
Ref. acta crystallogr ,sect b, 1992, 48, 59.
Secondary reference #5
Title Binding modes of a new epoxysuccinyl-Peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
Authors C.Czaplewski, Z.Grzonka, M.Jaskólski, F.Kasprzykowski, M.Kozak, E.Politowska, J.Ciarkowski.
Ref. Biochim Biophys Acta, 1999, 1431, 290-305. [DOI no: 10.1016/S0167-4838(99)00053-9]
PubMed id 10350606
Full text Abstract
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