7Z58: Human Cathepsin L

Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin. Determined by X-ray diffraction at 1.35 Å resolution. Released 22 Mar 2023.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,359
Mol. weight: 100.05 kDa
Ligands: RN2
Released: 22 Mar 2023

Explore 7Z58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z58 contains 47 α-helices and 64 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	2
α-helix	25-42	18
β-strand	48	1	3
α-helix	50-56	7
α-helix	58-60	3
α-helix	64-66	3
α-helix	70-80	11
β-strand	83-84	2	4
β-strand	85	1	3
α-helix	102-104	3
β-strand	105-107	3	4
β-strand	112-114	3	1
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	1
α-helix	141-144	4
β-strand	150-151	2	1
β-strand	163-172	10	1
β-strand	181-186	6	1
β-strand	189	1	2
β-strand	195	1	1
β-strand	198-202	5	1
α-helix	208-210	3
β-strand	216-218	3	1

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	5
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	6
α-helix	25-42	18
β-strand	48	1	7
α-helix	50-56	7
α-helix	58-60	3
α-helix	64-66	3
α-helix	70-80	11
β-strand	83-84	2	8
β-strand	85	1	7
α-helix	102-104	3
β-strand	105-107	3	8
β-strand	112-114	3	5
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	5
α-helix	141-144	4
β-strand	150-151	2	5
β-strand	163-171	9	5
β-strand	182-186	5	5
β-strand	189	1	6
β-strand	195	1	5
β-strand	198-202	5	5
α-helix	208-210	3
β-strand	216-218	3	5

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	9
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	10
β-strand	23	1	11
α-helix	25-42	18
β-strand	48	1	12
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	11
α-helix	70-80	11
β-strand	83-84	2	13
β-strand	85	1	12
α-helix	102-104	3
β-strand	105-107	3	13
β-strand	112-114	3	9
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	9
α-helix	141-144	4
β-strand	150-151	2	9
β-strand	163-171	9	9
β-strand	182-186	5	9
β-strand	189	1	10
β-strand	195	1	9
β-strand	198-202	5	9
α-helix	208-210	3
β-strand	216-218	3	9

Chain D: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	14
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	15
β-strand	23	1	16
α-helix	25-42	18
β-strand	48	1	17
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	16
α-helix	70-80	11
β-strand	83-84	2	18
β-strand	85	1	17
α-helix	102-104	3
β-strand	105-107	3	18
β-strand	112-114	3	14
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	14
α-helix	141-144	4
β-strand	150-151	2	14
β-strand	163-172	10	14
α-helix	176-178	3
β-strand	181-186	6	14
β-strand	189	1	15
β-strand	195	1	14
β-strand	198-202	5	14
α-helix	208-210	3
β-strand	216-218	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cathepsin L	A, B, C, D	protein	220	Homo sapiens	P07711 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7Z58_1 Cathepsin L (chains A, B, C, D)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDAGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
RN2	Calpeptin	C20 H32 N2 O4	4

Water and common crystallization additives (PEG, PGE, EDO, DMS) are not listed.

Primary citation

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Reinke, P.Y.A., de Souza, E.E., Gunther, S. et al. Commun Biol (2023) 6:1058-1058. DOI 10.1038/s42003-023-05317-9 · PubMed

Other PDB entries of the same protein (UniProt P07711 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XU3 0.9 Å, Cathepsin L with a nitrile inhibitor
5MAE 1.0 Å, CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro…
5MAJ 1.0 Å, CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morp…
2XU4 1.12 Å, Cathepsin L with a nitrile inhibitor
5MQY 1.13 Å, CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluorop…
2YJC 1.14 Å, Cathepsin L with a nitrile inhibitor
2YJ2 1.15 Å, Cathepsin L with a nitrile inhibitor
3HHA 1.27 Å, Crystal structure of cathepsin L in complex with AZ12878478
2YJ8 1.3 Å, Cathepsin L with a nitrile inhibitor
2YJ9 1.35 Å, Cathepsin L with a nitrile inhibitor
6EZP 1.37 Å, CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4…
2YJB 1.4 Å, Cathepsin L with a nitrile inhibitor

Browse structure collections

About this viewer

MolViewer shows 7Z58 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.