PDB 7qkb structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

1.8Å resolution

Crystal structure of human Cathepsin L in complex with covalently bound GC376

Released: 28 Dec 2022

DOI: 10.2210/pdb7qkb/pdb

Source organism: Homo sapiens

Primary publication:
Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Reinke PYA, de Souza EE, Günther S, Falke S, Lieske J, Ewert W, Loboda J, Herrmann A, Rahmani Mashhour A, Karničar K, Usenik A, Lindič N, Sekirnik A, Botosso VF, Santelli GMM, Kapronezai J, de Araújo MV, Silva-Pereira TT, Filho AFS, Tavares MS, Flórez-Álvarez L, de Oliveira DBL, Durigon EL, Giaretta PR, Heinemann MB, Hauser M, Seychell B, Böhler H, Rut W, Drag M, Beck T, Cox R, Chapman HN, Betzel C, Brehm W, Hinrichs W, Ebert G, Latham SL, Guimarães AMS, Turk D, Wrenger C, Meents A

Commun Biol 6 1058 (2023)

PMID: 37853179

Function and Biology Details

Reaction catalysed:

Similar to that of papain. As compared to cathepsin B, cathepsin L exhibits higher activity toward protein substrates, but has little activity on Z-Arg-Arg-NHMec, and no peptidyl-dipeptidase activity.

Biochemical function:

cysteine-type peptidase activity

Biological process:

proteolysis

Cellular component:

not assigned

Sequence domains:

Structure analysis Details

Assembly composition:

monomeric (preferred)

Assembly name:

Procathepsin L (preferred)

PDBe Complex ID:

PDB-CPX-139718 (preferred)

Entry contents:

1 distinct polypeptide molecule

Macromolecule:

Cathepsin L Chains: A, B, C, D

Molecule details ›

Chains: A, B, C, D
Length: 220 amino acids
Theoretical weight: 24.16 KDa
Source organism: Homo sapiens
Expression system: Komagataella phaffii GS115
UniProt:

Canonical: P07711 (Residues: 114-333; Coverage: 70%)

Gene names: CTSL, CTSL1
Sequence domains: Papain family cysteine protease

Ligands and Environments

7 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores

X-ray source: PETRA III, DESY BEAMLINE P11

Spacegroup: P1

Unit cell:

a: 57.29Å b: 62.45Å c: 67.82Å

α: 105.306° β: 93.523° γ: 115.929°

R-values:

R R_work R_free

0.17 0.169 0.203

Expression system: Komagataella phaffii GS115

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Assembly 1 (mmCIF; gz)
Assembly 2 (mmCIF; gz)
Assembly 3 (mmCIF; gz)
Assembly 4 (mmCIF; gz)
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Citations

3 citation in other articles

Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity.

Flury et al. (2024)

2 more

2 mentions without citation

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Reinke et al. (2023)

1 more