Research workbench
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z100642432
Analyse ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7G8A
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Homo sapiens
- Molecule
- Transforming protein RhoA; Rho guanine nucleotide exchange factor 2
- EC
- 3.6.5.2
- UniProt
- P61586, Q92974
- Ligands
- WJ7
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming protein RhoA (EC 3.6.5.2) | protein | 179 | 37% helix, 23% strand | P61586 |
| B | Rho guanine nucleotide exchange factor 2 | protein | 245 | 74% helix, 0% strand | Q92974 |
Ligands and binding sites
- WJ7 · 2-bromo-4-fluoro-N,N-dimethylbenzamide · ligand · chains A, B
- FMT · Formic acid · additive · 15 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B
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 | 277 | 0.66 | 0.82 | 36 | empty |
| 2 | 301 | 0.61 | 0.79 | 31 | empty |
| 3 | 173 | 0.45 | 0.75 | 35 | FMT |
| 4 | 108 | 0.35 | 0.73 | 17 | WJ7, FMT |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- Q92974 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 2 (Q92974) · a predicted model of the same protein · chain B against A, TM-score 0.95
- 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 Q92974
- Elsewhere: RCSB PDB 7G8A · PDBe 7G8A · UniProt P61586 · UniProt Q92974
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