MolNFT v1 · #36847 · protein
Crystal structure of a bovine rabex-5 fragment complexed with ubiquitin
2FID: “Crystal structure of a bovine rabex-5 fragment complexed with ubiquitin”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.28). MolNFT v1 #36847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2FID
- Type
- protein
- Length
- 133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; RAB5 GDP/GTP exchange factor
- UniProt
- P62990, O18973
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 73 | 26% helix, 34% strand | P62990 |
| B | RAB5 GDP/GTP exchange factor | protein | 60 | 63% helix, 3% strand | O18973 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.28 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2FID · Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- O18973 · AlphaFold monomer V2.0 prediction for RAB5 GDP/GTP exchange factor (O18973) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P62990
- Every structure of UniProt O18973
- Elsewhere: RCSB PDB 2FID · PDBe 2FID · UniProt P62990 · UniProt O18973
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