Research workbench
Double acetylated rhogdi-alpha in complex with rhoa-GDP
Analyse Double acetylated rhogdi-alpha in complex with rhoa-GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FR1
- Type
- protein
- Length
- 351 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
- GDP, MG
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming protein rhoa | protein | 184 | 38% helix, 22% strand | P61586 |
| B | Rho GDP-dissociation inhibitor 1 | protein | 167 | 13% helix, 49% strand | P19803 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.48 | 0.80 | 24 | empty |
| 2 | 163 | 0.48 | 0.77 | 20 | empty |
| 3 | 109 | 0.43 | 0.77 | 25 | GDP, MG |
| 4 | 58 | 0.38 | 0.79 | 15 | empty |
| 5 | 51 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1570 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 5FR1 · Double acetylated RhoGDI-alpha in complex with RhoA-GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 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 0.92
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 5FR1 · PDBe 5FR1 · UniProt P61586 · UniProt P19803
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