8A4W: Cathepsin L

Crystal structure of human cathepsin L with covalently bound Cathepsin L inhibitor IV. Determined by X-ray diffraction at 1.4 Å resolution. Released 5 Jul 2023.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,372
Mol. weight: 99.91 kDa
Ligands: L2F
Released: 5 Jul 2023

Explore 8A4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A4W contains 45 α-helices and 70 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: 11 helices, 17 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
β-strand	23	1	3
α-helix	25-42	18
β-strand	48	1	4
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	3
α-helix	70-80	11
β-strand	83-84	2	5
β-strand	85	1	4
α-helix	102-104	3
β-strand	105-107	3	5
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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	7
β-strand	23	1	8
α-helix	25-42	18
β-strand	48	1	9
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	8
α-helix	70-80	11
β-strand	83-84	2	10
β-strand	85	1	9
α-helix	102-104	3
β-strand	105-107	3	10
β-strand	112-114	3	6
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	6
α-helix	141-144	4
β-strand	150-151	2	6
β-strand	163-171	9	6
β-strand	182-186	5	6
β-strand	189	1	7
β-strand	195	1	6
β-strand	198-202	5	6
α-helix	208-210	3
β-strand	216-218	3	6

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	11
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	12
β-strand	23	1	13
α-helix	25-42	18
β-strand	48	1	14
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	13
α-helix	70-80	11
β-strand	83-84	2	15
β-strand	85	1	14
α-helix	102-104	3
β-strand	105-107	3	15
β-strand	112-114	3	11
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	11
α-helix	141-144	4
β-strand	150-151	2	11
β-strand	163-171	9	11
β-strand	174	1	16
β-strand	177	1	16
β-strand	182-186	5	11
β-strand	189	1	12
β-strand	195	1	11
β-strand	198-202	5	11
α-helix	208-210	3
β-strand	216-218	3	11

Chain D: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	17
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	18
β-strand	23	1	19
α-helix	25-42	18
β-strand	48	1	20
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	19
α-helix	70-80	11
β-strand	83-84	2	21
β-strand	85	1	20
α-helix	102-104	3
β-strand	105-107	3	21
β-strand	112-114	3	17
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	17
α-helix	141-144	4
β-strand	150-151	2	17
β-strand	163-172	10	17
α-helix	176-178	3
β-strand	181-186	6	17
β-strand	189	1	18
β-strand	195	1	17
β-strand	198-202	5	17
α-helix	208-210	3
β-strand	216-218	3	17

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

>8A4W_1 Cathepsin L (chains A, B, C, D)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDAGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
L2F	N-(1-naphthylsulfonyl)-(L)-isoleucyl-(L)-tryptophanol	C27 H31 N3 O4 S	4

Water and common crystallization additives (PEG, EDO, DMS, PG4, NA) are not listed.

Primary citation

Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. Falke, S., Lieske, J., Herrmann, A. et al. J Med Chem (2024) 67:7048-7067. DOI 10.1021/acs.jmedchem.3c02351 · 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
7Z58 1.35 Å, Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin
6EZP 1.37 Å, CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4…

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