Research workbench
Crystal structure of isoprene synthase from grey poplar leaves (populus X canescens) in complex with three MG2+ ions and dimethylallyl-S-thiolodiphosphate
Analyse Crystal structure of isoprene synthase from grey poplar leaves (populus X… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N0G
- Type
- protein
- Length
- 1,045 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoprene synthase
- EC
- 4.2.3.27
- UniProt
- Q9AR86
- Ligands
- DST, MG
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoprene synthase (EC 4.2.3.27) | protein | 521 | 76% helix, 0% strand | Q9AR86 |
| B | Isoprene synthase (EC 4.2.3.27) | protein | 524 | 72% helix, 0% strand | Q9AR86 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.78 | 0.86 | 43 | empty |
| 2 | 470 | 0.78 | 0.86 | 39 | empty |
| 3 | 505 | 0.68 | 0.78 | 52 | DST, MG |
| 4 | 286 | 0.66 | 0.82 | 34 | empty |
| 5 | 424 | 0.66 | 0.79 | 50 | DST, MG |
Interfaces
1 interface between chains.
- A–B · 369 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3N0G · Crystal Structure of Isoprene Synthase from Grey Poplar Leaves (Populus x canescens) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AR86 · AlphaFold monomer V2.0 prediction for isoprene synthase, chloroplastic (Q9AR86) · 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 Q9AR86
- Elsewhere: RCSB PDB 3N0G · PDBe 3N0G · UniProt Q9AR86
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