2XU1: Cathepsin L with a nitrile inhibitor

Cathepsin L with a nitrile inhibitor. Determined by X-ray diffraction at 1.45 Å resolution. Released 12 Jan 2011.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,696
Mol. weight: 98.78 kDa
Ligands: 424
Released: 12 Jan 2011

Explore 2XU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XU1 contains 44 α-helices and 66 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: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
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	119-128	10
β-strand	132-136	5	1
α-helix	141-144	4
β-strand	150-151	2	1
β-strand	163-171	9	1
β-strand	182-186	5	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, 17 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
β-strand	23	1	7
α-helix	25-42	18
β-strand	48	1	8
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	7
α-helix	70-80	11
β-strand	83-84	2	9
β-strand	85	1	8
α-helix	102-104	3
β-strand	105-107	3	9
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	163-172	10	5
α-helix	176-178	3
β-strand	181-186	6	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	10
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	11
β-strand	23	1	12
α-helix	25-42	18
β-strand	48	1	13
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	12
α-helix	70-80	11
β-strand	83-84	2	14
β-strand	85	1	13
α-helix	102-104	3
β-strand	105-107	3	14
β-strand	112-114	3	10
α-helix	115-116	2
α-helix	119-129	11
β-strand	132-136	5	10
α-helix	141-145	5
β-strand	150-151	2	10
β-strand	163-172	10	10
β-strand	181-186	6	10
β-strand	189	1	11
β-strand	195	1	10
β-strand	198-202	5	10
α-helix	208-210	3
β-strand	216-218	3	10

Chain D: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	15
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	16
β-strand	23	1	17
α-helix	25-42	18
β-strand	48	1	18
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	17
α-helix	70-80	11
β-strand	83-84	2	19
β-strand	85	1	18
α-helix	102-104	3
β-strand	105-107	3	19
β-strand	112-114	3	15
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	15
α-helix	141-145	5
β-strand	150-151	2	15
β-strand	163-171	9	15
β-strand	182-186	5	15
β-strand	189	1	16
β-strand	195	1	15
β-strand	198-202	5	15
α-helix	208-210	3
β-strand	216-218	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cathepsin L1	A, B, C, D	protein	220	HOMO SAPIENS	P07711 (AlphaFold model)

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

>2XU1_1 CATHEPSIN L1 (chains A, B, C, D)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDAGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
424	(2S,4R)-1-[1-(4-chlorophenyl)cyclopropyl]carbonyl-4-(2-chlorophenyl)sulfonyl-N-…	C25 H25 Cl2 N3 O4 S	4

Primary citation

Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions. Hardegger, L.A., Kuhn, B., Spinnler, B. et al. Angew Chem Int Ed Engl (2011) 50:314. DOI 10.1002/ANIE.201006781 · 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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