Research workbench
Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 37)
Analyse Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 37) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HXE
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Rattus norvegicus
- Molecule
- Geranylgeranyl transferase type-2 subunit alpha; Geranylgeranyl transferase type-2…
- EC
- 2.5.1.60
- UniProt
- Q08602, Q08603
- Ligands
- BD8, ZN, CA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.95 · 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 | 306 | 79% 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
- BD8 · N-undecanoyl-L-histidyl-L-phenylalanyl-N-methyl-N-(2-pyridin-2-ylethyl)-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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.80 | 0.81 | 94 | BD8 |
| 2 | 164 | 0.55 | 0.80 | 26 | empty |
| 3 | 224 | 0.54 | 0.77 | 34 | empty |
| 4 | 179 | 0.52 | 0.79 | 22 | empty |
| 5 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2183 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3HXE · Engineered rabggtase in complex with a peptidomimetic inhibitor (compound 37) · 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 0.97
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 3HXE · PDBe 3HXE · UniProt Q08602 · UniProt Q08603
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