MolNFT v1 · #37807 · protein
Structural basis for budding by the escrtiii factor CHMP3
2GD5 · Charged multivesicular body protein 3: “Structural basis for budding by the escrtiii factor CHMP3”. X-ray diffraction, 6 pockets (best druggability 0.63). MolNFT v1 #37807 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2GD5
- Type
- protein
- Length
- 602 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Charged multivesicular body protein 3
- UniProt
- Q9Y3E7
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Charged multivesicular body protein 3 | protein | 142 | 73% helix, 0% strand | Q9Y3E7 |
| B | Charged multivesicular body protein 3 | protein | 156 | 72% helix, 0% strand | Q9Y3E7 |
| C | Charged multivesicular body protein 3 | protein | 142 | 81% helix, 0% strand | Q9Y3E7 |
| D | Charged multivesicular body protein 3 | protein | 162 | 73% helix, 0% strand | Q9Y3E7 |
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 | 280 | 0.63 | 0.80 | 38 | empty |
| 2 | 147 | 0.57 | 0.83 | 23 | empty |
| 3 | 147 | 0.56 | 0.82 | 25 | empty |
| 4 | 196 | 0.52 | 0.78 | 25 | empty |
| 5 | 176 | 0.49 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1867 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1806 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 47 modified (engineered).
Compared structures
- 2GD5 · Structural basis for budding by the ESCRTIII factor CHMP3 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y3E7 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 3 (Q9Y3E7) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q9Y3E7
- Elsewhere: RCSB PDB 2GD5 · PDBe 2GD5 · UniProt Q9Y3E7
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