MolNFT v1 · #35573 · protein
ARA7/ATVPS9A
2EFD · Similarity to vacuolar protein sorting-associated protein…: “ARA7/ATVPS9A”. X-ray diffraction, 12 pockets (best druggability 0.61). MolNFT v1 #35573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2EFD
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similarity to vacuolar protein sorting-associated protein VPS9; Small GTP-binding…
- UniProt
- Q9LT31, Q9SN68
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Similarity to vacuolar protein sorting-associated protein VPS9 | protein | 246 | 72% helix, 0% strand | Q9LT31 |
| B, D | Small GTP-binding protein-like | protein | 152 | 34% helix, 27% strand | Q9SN68 |
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.61 | 0.80 | 36 | empty |
| 2 | 174 | 0.52 | 0.78 | 26 | empty |
| 3 | 135 | 0.48 | 0.78 | 26 | empty |
| 4 | 156 | 0.47 | 0.76 | 19 | empty |
| 5 | 108 | 0.44 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1035 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1035 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 625 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2EFD · Ara7/AtVps9a · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LT31 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 9A… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9SN68 · AlphaFold monomer V2.0 prediction for RAS-related protein RABF2B (Q9SN68) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9LT31
- Every structure of UniProt Q9SN68
- Elsewhere: RCSB PDB 2EFD · PDBe 2EFD · UniProt Q9LT31 · UniProt Q9SN68
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