6JD8: Proline specific mutant of human cathepsin L

Structure of a proline specific mutant of human cathepsin L. Determined by X-ray diffraction at 1.46 Å resolution. Released 5 Feb 2020.

Method: X-ray diffraction
Resolution: 1.46 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,878
Mol. weight: 41.88 kDa
Ligands: EOH
Released: 5 Feb 2020

Explore 6JD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JD8 contains 16 α-helices and 20 β-strands across 1 chain. 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: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-18	10
α-helix	28-50	23
β-strand	56-58	3	1
α-helix	68-74	7
β-strand	87-88	2	2
α-helix	89	1
α-helix	91-92	2
β-strand	101-102	2	2
α-helix	103-106	4
α-helix	110-112	3
β-strand	114	1	3
β-strand	119	1	4
α-helix	121-138	18
β-strand	144	1	5
α-helix	146-152	7
β-strand	162	1	4
α-helix	166-176	11
β-strand	179-180	2	6
β-strand	181	1	5
α-helix	198-200	3
β-strand	201-203	3	6
β-strand	208-210	3	2
α-helix	211-212	2
α-helix	215-225	11
β-strand	228-232	5	2
α-helix	237-240	4
β-strand	242-245	4	1
β-strand	246-247	2	2
β-strand	259-268	10	2
β-strand	277-282	6	2
β-strand	285	1	3
β-strand	291	1	2
β-strand	294-298	5	2
α-helix	304-306	3
β-strand	312-314	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cathepsin L1	A	protein	360	Homo sapiens	P07711 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6JD8_1 Cathepsin L1 (chains A)
MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKMTLTFDHSLEAQWTKWK
AMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMN
GFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSSWAFSATGALEGQMFR
KTGRLISLSEQNLVDCSGPQGNEGCNGGYMDYAFQYVQDNGGLDSEESYPYEATEESCKY
NPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSED
LDHAVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASLASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
EOH	Ethanol	C2 H6 O	12

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

Primary citation

Structure-guided protein engineering of human cathepsin L for efficient collagenolytic activity. Choudhury, D., Biswas, S. Protein Eng Des Sel (2021) 34. DOI 10.1093/protein/gzab005 · 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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