MolNFT v1 · #162267 · protein
Crystal structure of rhoa-GDP-pi in complex with rhogap
6R3V · Rho GTPase-activating protein 1: “Crystal structure of rhoa-GDP-pi in complex with rhogap”. X-ray diffraction, 3 ligands (GDP, MG, PO4), 3 pockets (best druggability 0.67). MolNFT v1 #162267 on GenesisL1: 3D structure, binding sites…
- PDB
- 6R3V
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- 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, MG, PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho GTPase-activating protein 1 | protein | 198 | 65% helix, 0% strand | Q07960 |
| B | Transforming protein rhoa | protein | 172 | 38% helix, 26% strand | P61586 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.67 | 0.78 | 57 | GDP, MG, PO4 |
| 2 | 86 | 0.39 | 0.77 | 26 | empty |
| 3 | 59 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1264 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6R3V · Crystal Structure of RhoA-GDP-Pi in Complex with RhoGAP · 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 1.00
- 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 6R3V · PDBe 6R3V · UniProt Q07960 · UniProt P61586
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