MolNFT v1 · #117450 · protein
Crystal structure of geranylgeranyl pyrophosphate synthase 11 from arabidopsis thaliana
5E8L · Heterodimeric geranylgeranyl pyrophosphate synthase large…: “Crystal structure of geranylgeranyl pyrophosphate synthase 11 from arabidopsis thaliana”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #117450 on…
- PDB
- 5E8L
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic
- EC
- 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10
- UniProt
- P34802
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 278 | 70% helix, 1% strand | P34802 |
| B | Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 281 | 69% helix, 1% strand | P34802 |
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 | 541 | 0.71 | 0.80 | 59 | empty |
| 2 | 386 | 0.63 | 0.78 | 47 | empty |
| 3 | 51 | 0.55 | 0.90 | 14 | empty |
| 4 | 68 | 0.37 | 0.78 | 13 | empty |
| 5 | 57 | 0.34 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5E8L · Crystal structure of geranylgeranyl pyrophosphate synthase 11 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- P34802 · AlphaFold monomer V2.0 prediction for heterodimeric geranylgeranyl pyrophosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P34802
- Elsewhere: RCSB PDB 5E8L · PDBe 5E8L · UniProt P34802
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