MolNFT v1 · #75728 · protein
Crystal structure of RABGGTASE(DELTA lrr; delta ig) in complex with BMS3 and lipid substrate ggpp
3PZ2 · Geranylgeranyl transferase type-2 subunit alpha: “Crystal structure of RABGGTASE(DELTA lrr; delta ig) in complex with BMS3 and lipid substrate ggpp”. X-ray diffraction, 4 ligands (3PZ, GRG, ZN), 6 pockets (best druggability 0.80).…
- PDB
- 3PZ2
- Type
- protein
- Length
- 620 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
- 3PZ, GRG, ZN, CA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl transferase type-2 subunit alpha (EC 2.5.1.60) | protein | 298 | 78% helix, 0% strand | Q08602 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 322 | 50% helix, 5% strand | Q08603 |
Ligands and binding sites
- 3PZ · (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile · ligand · chains A, B
- GRG · Geranylgeranyl diphosphate · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.80 | 0.81 | 90 | 3PZ, GRG |
| 2 | 198 | 0.55 | 0.79 | 38 | empty |
| 3 | 139 | 0.47 | 0.78 | 20 | empty |
| 4 | 149 | 0.41 | 0.74 | 21 | empty |
| 5 | 64 | 0.37 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2187 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3PZ2 · Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid… · 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 0.94
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 3PZ2 · PDBe 3PZ2 · UniProt Q08602 · UniProt Q08603
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