MolNFT v1 · #37502 · protein
Crystal structure of the C-terminal domain of VPS28
2G3K · Vacuolar protein sorting-associated protein VPS28: “Crystal structure of the C-terminal domain of VPS28”. X-ray diffraction, 6 pockets (best druggability 0.85). MolNFT v1 #37502 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2G3K
- Type
- protein
- Length
- 658 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein VPS28
- UniProt
- Q02767
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Vacuolar protein sorting-associated protein VPS28 | protein | 94 | 73% helix, 2% strand | Q02767 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.85 | 0.86 | 91 | empty |
| 2 | 559 | 0.74 | 0.81 | 48 | empty |
| 3 | 132 | 0.62 | 0.86 | 17 | empty |
| 4 | 199 | 0.51 | 0.77 | 37 | empty |
| 5 | 104 | 0.41 | 0.77 | 19 | empty |
Interfaces
14 interfaces between chains.
- A–B · 823 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 648 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 626 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 462 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 2G3K · Crystal structure of the C-terminal domain of Vps28 · the same entry in another collection · chain G against G, TM-score 1.00
- Q02767 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 28… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02767
- Elsewhere: RCSB PDB 2G3K · PDBe 2G3K · UniProt Q02767
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