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Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate
Analyse Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P41
- Type
- protein
- Length
- 283 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyltranstransferase
- UniProt
- Q4K5A6
- Ligands
- DMA, POP, MG, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyltranstransferase | protein | 283 | 75% helix, 1% strand | Q4K5A6 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.65 | 0.78 | 47 | MG, DMA, POP |
| 2 | 112 | 0.36 | 0.73 | 19 | empty |
| 3 | 51 | 0.33 | 0.78 | 8 | empty |
Modifications
Observed in the structure: 8 modified (engineered, acetylation).
Compared structures
- 3P41 · Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed… · 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 Q4K5A6
- Elsewhere: RCSB PDB 3P41 · PDBe 3P41 · UniProt Q4K5A6
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