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Native structure of farnesyl pyrophosphate synthase from pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate.
Analyse Native structure of farnesyl pyrophosphate synthase from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOU
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q9HWY4
- Ligands
- 6H6, GPP, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 274 | 75% helix, 1% strand | Q9HWY4 |
| B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 273 | 75% helix, 1% strand | Q9HWY4 |
Ligands and binding sites
- 6H6 · 3-(2-oxo-1,3-benzoxazol-3(2H)-yl)propanoic acid · ligand · 2 copies · chains A, B
- GPP · Geranyl diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- DMS · Dimethyl sulfoxide · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.70 | 0.80 | 60 | GPP, MG, 6H6 |
| 2 | 386 | 0.60 | 0.76 | 47 | 6H6, MG, DMS |
| 3 | 226 | 0.52 | 0.76 | 29 | GOL |
| 4 | 55 | 0.49 | 0.86 | 15 | empty |
| 5 | 172 | 0.48 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1909 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ZOU · Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9HWY4
- Elsewhere: RCSB PDB 3ZOU · PDBe 3ZOU · UniProt Q9HWY4
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