Research workbench
Crystal structure of polyprenyl pyrophosphate synthase 2 from arabidopsis thaliana
Analyse Crystal structure of polyprenyl pyrophosphate synthase 2 from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8K
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase 10, mitochondrial
- EC
- 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10
- UniProt
- Q9LJY2
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase 10, mitochondrial (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 270 | 71% helix, 1% strand | Q9LJY2 |
| B | Geranylgeranyl pyrophosphate synthase 10, mitochondrial (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 268 | 65% helix, 1% strand | Q9LJY2 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.70 | 0.79 | 52 | empty |
| 2 | 121 | 0.61 | 0.86 | 21 | empty |
| 3 | 378 | 0.58 | 0.75 | 41 | empty |
| 4 | 135 | 0.47 | 0.78 | 26 | empty |
| 5 | 99 | 0.44 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1460 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5E8K · Crystal structure of polyprenyl pyrophosphate synthase 2 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LJY2 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase 10… · 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 Q9LJY2
- Elsewhere: RCSB PDB 5E8K · PDBe 5E8K · UniProt Q9LJY2
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