MolNFT v1 · #117446 · protein
Crystal structure of geranylfarnesyl pyrophosphate synthases 2 from arabidopsis thaliana
5E8H · Geranylgeranyl pyrophosphate synthase 3, chloroplastic: “Crystal structure of geranylfarnesyl pyrophosphate synthases 2 from arabidopsis thaliana”. X-ray diffraction, 7 pockets (best druggability 0.64). MolNFT v1 #117446 on…
- PDB
- 5E8H
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase 3, chloroplastic
- EC
- 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10
- UniProt
- Q9LUD9
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase 3, chloroplastic (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 278 | 76% helix, 1% strand | Q9LUD9 |
| B | Geranylgeranyl pyrophosphate synthase 3, chloroplastic (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 270 | 77% helix, 1% strand | Q9LUD9 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.64 | 0.93 | 21 | empty |
| 2 | 303 | 0.60 | 0.78 | 39 | empty |
| 3 | 355 | 0.60 | 0.77 | 43 | empty |
| 4 | 57 | 0.34 | 0.78 | 21 | empty |
| 5 | 60 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1855 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5E8H · Crystal structure of geranylfarnesyl pyrophosphate synthases 2 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LUD9 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase 3… · 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 Q9LUD9
- Elsewhere: RCSB PDB 5E8H · PDBe 5E8H · UniProt Q9LUD9
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