Research workbench
Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
Analyse Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OT3
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAB5 GDP/GTP exchange factor; RAS-related protein rab-21
- UniProt
- Q9UJ41, Q9UL25
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAB5 GDP/GTP exchange factor | protein | 253 | 72% helix, 0% strand | Q9UJ41 |
| B | RAS-related protein rab-21 | protein | 157 | 41% helix, 29% strand | Q9UL25 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.54 | 0.78 | 26 | empty |
| 2 | 77 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1176 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2OT3 · Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJ41 · AlphaFold monomer V2.0 prediction for RAB5 GDP/GTP exchange factor (Q9UJ41) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UL25 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-21 (Q9UL25) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9UJ41
- Every structure of UniProt Q9UL25
- Elsewhere: RCSB PDB 2OT3 · PDBe 2OT3 · UniProt Q9UJ41 · UniProt Q9UL25
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