MolNFT v1 · #66667 · protein
Engineered rabggtase in complex with a peptidomimetic inhibitor (compound 6)
3HXB · Geranylgeranyl transferase type-2 subunit alpha: “Engineered rabggtase in complex with a peptidomimetic inhibitor (compound 6)”. X-ray diffraction, 2 ligands (BD5, ZN), 8 pockets (best druggability 0.79). MolNFT v1 #66667 on…
- PDB
- 3HXB
- 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
- BD5, ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 64% 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 | 78% helix, 0% strand | Q08602 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 324 | 51% helix, 6% strand | Q08603 |
Ligands and binding sites
- BD5 · N-[(benzyloxy)carbonyl]-D-tyrosyl-L-phenylalanyl-L-tyrosine · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.79 | 0.80 | 91 | BD5, ZN |
| 2 | 229 | 0.55 | 0.78 | 36 | empty |
| 3 | 246 | 0.54 | 0.76 | 35 | empty |
| 4 | 95 | 0.49 | 0.81 | 19 | empty |
| 5 | 171 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2112 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3HXB · Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 6) · the same entry in another collection · chain A against A, 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 0.96
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 3HXB · PDBe 3HXB · UniProt Q08602 · UniProt Q08603
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