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Cysteine protease ATG4A

Analyse Cysteine protease ATG4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P82
Type: protein
Length: 1,232 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine protease ATG4A
EC: 3.4.22.-
UniProt: Q8WYN0
Ligands: CL
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine protease ATG4A (EC 3.4.22.-)	protein	312	31% helix, 24% strand	Q8WYN0
B	Cysteine protease ATG4A (EC 3.4.22.-)	protein	312	32% helix, 23% strand	Q8WYN0
C	Cysteine protease ATG4A (EC 3.4.22.-)	protein	307	33% helix, 22% strand	Q8WYN0
D	Cysteine protease ATG4A (EC 3.4.22.-)	protein	301	33% helix, 23% strand	Q8WYN0

Ligands and binding sites

CL · Chloride ion · ion · chains D
EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.72	0.76	79	EDO
2	862	0.72	0.77	73	EDO
3	514	0.67	0.78	72	empty
4	392	0.66	0.79	46	empty
5	288	0.65	0.82	34	empty

Interfaces

6 interfaces between chains.

A–B · 1299 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1083 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 180 Å² buried · 1 hydrogen bond · protein-protein
A–C · 145 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 92 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2P82 · Cysteine protease ATG4A · the same entry in another collection · chain D against D, TM-score 1.00
Q8WYN0 · AlphaFold monomer V2.0 prediction for cysteine protease ATG4A (Q8WYN0) · a predicted model of the same protein · chain D against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8WYN0
Elsewhere: RCSB PDB 2P82 · PDBe 2P82 · UniProt Q8WYN0

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