MolNFT v1 · #55953 · protein
The crystal structure of human ATG4B- LC3(1-120) complex
2Z0D · Cysteine protease ATG4B: “The crystal structure of human ATG4B- LC3(1-120) complex”. X-ray diffraction, 4 pockets (best druggability 0.51). MolNFT v1 #55953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z0D
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease ATG4B; Microtubule-associated proteins 1A/1B light chain 3B
- EC
- 3.4.22.-
- UniProt
- Q9Y4P1, Q62625
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine protease ATG4B (EC 3.4.22.-) | protein | 309 | 33% helix, 21% strand | Q9Y4P1 |
| B | Microtubule-associated proteins 1A/1B light chain 3B | protein | 116 | 32% helix, 24% strand | Q62625 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.51 | 0.81 | 27 | empty |
| 2 | 88 | 0.36 | 0.75 | 16 | empty |
| 3 | 95 | 0.33 | 0.73 | 20 | empty |
| 4 | 57 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1296 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2Z0D · The crystal structure of human Atg4B- LC3(1-120) complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4P1 · AlphaFold monomer V2.0 prediction for cysteine protease ATG4B (Q9Y4P1) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q62625 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9Y4P1
- Every structure of UniProt Q62625
- Elsewhere: RCSB PDB 2Z0D · PDBe 2Z0D · UniProt Q9Y4P1 · UniProt Q62625
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