Research workbench
Crystal structure of human rhogap mutated in its arginin finger (R85A) in complex with RHOA.GDP.ALF4- human
Analyse Crystal structure of human rhogap mutated in its arginin finger (R85A) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M70
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho GTPase-activating protein 1; Transforming protein rhoa
- UniProt
- Q07960, P61586
- Ligands
- GDP, ALF, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Rho GTPase-activating protein 1 | protein | 188 | 68% helix, 0% strand | Q07960 |
| B, G | Transforming protein rhoa | protein | 172 | 40% helix, 24% strand | P61586 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, G
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains B, G
- MG · Magnesium ion · metal · 2 copies · chains B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.81 | 0.85 | 80 | empty |
| 2 | 398 | 0.75 | 0.85 | 56 | MG, GDP, ALF |
| 3 | 84 | 0.73 | 0.97 | 22 | empty |
| 4 | 181 | 0.67 | 0.86 | 37 | MG, GDP, ALF |
| 5 | 180 | 0.67 | 0.86 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1206 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1202 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 546 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 240 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5M70 · Crystal Structure of human RhoGAP mutated in its arginin finger (R85A) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07960 · AlphaFold monomer V2.0 prediction for rho GTPase-activating protein 1 (Q07960) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q07960
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 5M70 · PDBe 5M70 · UniProt Q07960 · UniProt P61586
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.