SMTL ID : 9ckw.1

X-ray diffraction structure of papain co-crystallized with E-64D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MOH: METHANOL(Non-functional Binders)

MOH.1: 2 residues within 4Å: Chain A: Y.78, Y.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.103

1 x E6D: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate(Covalent)

E6D.2: 13 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, Y.61, G.65, G.66, Y.67, V.133, D.158, H.159, A.160 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.61, A:Y.67, A:V.133, A:A.160 Hydrogen bonds: A:Q.19, A:C.25, A:G.66, A:G.66, A:D.158 Salt bridges: A:H.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, M. et al., Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors. Nat.Chem.Biol. (2025)

Release Date

2025-06-04

Peptides

Papain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain

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