MolNFT v1 · #128427 · protein
Structure of human ATG5-ATG16L1(ATG5BD) complex (I4)
5NPV · Autophagy protein 5: “Structure of human ATG5-ATG16L1(ATG5BD) complex (I4)”. X-ray diffraction, 4 pockets (best druggability 0.72). MolNFT v1 #128427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NPV
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy protein 5; Autophagy-related protein 16-1
- UniProt
- Q9H1Y0, Q676U5
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autophagy protein 5 | protein | 255 | 35% helix, 19% strand | Q9H1Y0 |
| B | Autophagy-related protein 16-1 | protein | 38 | 87% helix, 0% strand | Q676U5 |
| C | Autophagy protein 5 | protein | 237 | 37% helix, 19% strand | Q9H1Y0 |
| D | Autophagy-related protein 16-1 | protein | 39 | 90% helix, 0% strand | Q676U5 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.72 | 0.80 | 52 | empty |
| 2 | 167 | 0.51 | 0.78 | 29 | empty |
| 3 | 89 | 0.38 | 0.77 | 16 | empty |
| 4 | 65 | 0.33 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1169 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 299 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NPV · Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9H1Y0 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q9H1Y0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q676U5 · AlphaFold monomer V2.0 prediction for autophagy-related protein 16-1 (Q676U5) · a predicted model of the same protein · chain D against A, TM-score 0.66
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 Q9H1Y0
- Every structure of UniProt Q676U5
- Elsewhere: RCSB PDB 5NPV · PDBe 5NPV · UniProt Q9H1Y0 · UniProt Q676U5
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