SMTL ID : 7z58.3 (3 other biounits)

Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: F.39, R.40, K.41, T.42, G.43 No protein-ligand interaction detected (PLIP) PEG.2: 10 residues within 4Å: Chain A: A.138, G.139, H.140, E.141, F.143, L.144, D.162, H.163, W.189 Ligands: PGE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.140, A:D.162

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 9 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: PEG.2, RN2.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.19, A:Q.19

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: S.88, Y.89, P.90, K.99, N.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88

1 x RN2: Calpeptin(Covalent)

RN2.5: 21 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.61, N.62, E.63, C.65, N.66, G.67, G.68, L.69, M.70, Y.72, A.135, M.161, D.162, H.163, G.164 Ligands: PGE.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.69 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:G.68, A:D.162 Water bridges: A:Q.19, A:H.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reinke, P.Y.A. et al., Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol (2023)

Release Date

2023-03-22

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Cathepsin L

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