Research workbench
ARA7-GDP/ATVPS9A(D185N)
Analyse ARA7-GDP/ATVPS9A(D185N) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EFH
- 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
- Ligands
- GDP
- Pockets
- 9 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Similarity to vacuolar protein sorting-associated protein VPS9 | protein | 246 | 73% helix, 0% strand | Q9LT31 |
| B, D | Small GTP-binding protein-like | protein | 152 | 38% helix, 28% strand | Q9SN68 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.53 | 0.77 | 30 | empty |
| 2 | 155 | 0.48 | 0.77 | 30 | GDP |
| 3 | 142 | 0.48 | 0.78 | 33 | GDP |
| 4 | 99 | 0.37 | 0.74 | 17 | empty |
| 5 | 84 | 0.36 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1011 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1002 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 71 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 60 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2EFH · Ara7-GDP/AtVps9a(D185N) · the same entry in another collection · chain A against A, 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 0.97
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 2EFH · PDBe 2EFH · UniProt Q9LT31 · UniProt Q9SN68
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