MolNFT v1 · #66669 · protein
Engineered rabggtase in complex with a peptidomimetic inhibitor (compound 9)
3HXD · Geranylgeranyl transferase type-2 subunit alpha: “Engineered rabggtase in complex with a peptidomimetic inhibitor (compound 9)”. X-ray diffraction, 3 ligands (BD7, ZN, CA), 5 pockets (best druggability 0.80). MolNFT v1 #66669 on…
- PDB
- 3HXD
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl transferase type-2 subunit alpha; Geranylgeranyl transferase type-2…
- EC
- 2.5.1.60
- UniProt
- Q08602, Q08603
- Ligands
- BD7, ZN, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl transferase type-2 subunit alpha (EC 2.5.1.60) | protein | 308 | 80% helix, 0% strand | Q08602 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 324 | 52% helix, 5% strand | Q08603 |
Ligands and binding sites
- BD7 · N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tyrosinamide · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
- CA · Calcium ion · metal · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.80 | 0.81 | 98 | BD7 |
| 2 | 238 | 0.57 | 0.78 | 36 | empty |
| 3 | 217 | 0.54 | 0.78 | 33 | empty |
| 4 | 197 | 0.54 | 0.79 | 23 | empty |
| 5 | 73 | 0.28 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2174 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3HXD · Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 9) · the same entry in another collection · chain B against B, TM-score 1.00
- Q08603 · AlphaFold monomer V2.0 prediction for geranylgeranyl transferase type-2 subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q08602 · AlphaFold monomer V2.0 prediction for geranylgeranyl transferase type-2 subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q08602
- Every structure of UniProt Q08603
- Elsewhere: RCSB PDB 3HXD · PDBe 3HXD · UniProt Q08602 · UniProt Q08603
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.