MolNFT v1 · #21391 · protein
Crystal structure of RAB9 complexed to GDP reveals a dimer with an active conformation of switch II
1S8F · RAS-related protein rab-9A: “Crystal structure of RAB9 complexed to GDP reveals a dimer with an active conformation of switch II”. X-ray diffraction, 5 ligands (BEZ, GDP, SR), 3 pockets (best druggability 0.52). MolNFT v1 #21391 on…
- PDB
- 1S8F
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-9A
- UniProt
- P24408
- Ligands
- BEZ, GDP, SR, MG, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-9A | protein | 168 | 36% helix, 28% strand | P24408 |
| B | RAS-related protein rab-9A | protein | 173 | 34% helix, 29% strand | P24408 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 4 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SR · Strontium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.52 | 0.87 | 18 | BEZ |
| 2 | 177 | 0.52 | 0.78 | 36 | MG |
| 3 | 205 | 0.50 | 0.76 | 32 | SR, GDP, BEZ |
Interfaces
1 interface between chains.
- A–B · 890 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1S8F · Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of… · the same entry in another collection · chain A against A, TM-score 1.00
- P24408 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-9A (P24408) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P24408
- Elsewhere: RCSB PDB 1S8F · PDBe 1S8F · UniProt P24408
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