MolNFT v1 · #191393 · protein
Cryo-EM structure of a hops core complex containing VPS33, VPS16, and VPS18
8DIT · Vacuolar protein sorting-associated protein 33: “Cryo-EM structure of a hops core complex containing VPS33, VPS16, and VPS18”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #191393 on GenesisL1: 3D structure…
- PDB
- 8DIT
- Type
- protein
- Length
- 2,190 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 33; Vacuolar protein sorting-associated…
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 33 | protein | 620 | 49% helix, 12% strand | — |
| B | Vacuolar protein sorting-associated protein 16 | protein | 834 | 43% helix, 18% strand | — |
| C | Vacuolar protein sorting-associated protein 18 | protein | 736 | 42% helix, 21% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.80 | 0.85 | 60 | empty |
| 2 | 1084 | 0.78 | 0.80 | 112 | empty |
| 3 | 886 | 0.78 | 0.81 | 66 | empty |
| 4 | 271 | 0.71 | 0.86 | 44 | empty |
| 5 | 62 | 0.71 | 0.97 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3424 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2173 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 8DIT · Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18 · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 8DIT · PDBe 8DIT
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