MolNFT v1 · #119273 · protein
Farnesylated rhoa-GDP in complex with rhogdi-alpha, lysine acetylated at K178
5FR2 · Transforming protein rhoa: “Farnesylated rhoa-GDP in complex with rhogdi-alpha, lysine acetylated at K178”. X-ray diffraction, 4 ligands (FAR, GDP, BGC), 4 pockets (best druggability 0.79). MolNFT v1 #119273 on GenesisL1: 3D…
- PDB
- 5FR2
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein rhoa; Rho GDP-dissociation inhibitor 1
- UniProt
- P61586, P19803
- Ligands
- FAR, GDP, BGC, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming protein rhoa | protein | 187 | 37% helix, 25% strand | P61586 |
| B | Rho GDP-dissociation inhibitor 1 | protein | 178 | 12% helix, 43% strand | P19803 |
Ligands and binding sites
- FAR · Farnesyl · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.79 | 0.95 | 31 | FAR |
| 2 | 371 | 0.60 | 0.76 | 56 | empty |
| 3 | 117 | 0.44 | 0.77 | 25 | GDP, MG |
| 4 | 79 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1498 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid, 1 modified (farnesylation, acetylation).
Compared structures
- 5FR2 · Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetylated at K178 · the same entry in another collection · chain A against A, TM-score 1.00
- P19803 · AlphaFold monomer V2.0 prediction for rho GDP-dissociation inhibitor 1 (P19803) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P61586
- Every structure of UniProt P19803
- Elsewhere: RCSB PDB 5FR2 · PDBe 5FR2 · UniProt P61586 · UniProt P19803
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