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Crystal structure of a farnesyl diphosphate synthase from roseobacter denitrificans och 114, target efi-509393, with ipp, gspp, and calcium bound in active site
Analyse Crystal structure of a farnesyl diphosphate synthase from roseobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LLS
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyltranstransferase
- EC
- 2.5.1.10
- UniProt
- Q16CN9
- Ligands
- IPE, GST, CA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyltranstransferase (EC 2.5.1.10) | protein | 300 | 75% helix, 1% strand | Q16CN9 |
| B | Geranyltranstransferase (EC 2.5.1.10) | protein | 290 | 76% helix, 1% strand | Q16CN9 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- GST · Geranyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.83 | 0.89 | 60 | IPE, GST, CA |
| 2 | 456 | 0.82 | 0.89 | 57 | IPE, GST, CA |
| 3 | 184 | 0.47 | 0.75 | 29 | empty |
| 4 | 149 | 0.43 | 0.75 | 28 | empty |
| 5 | 52 | 0.38 | 0.80 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1845 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4LLS · Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh… · 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 Q16CN9
- Elsewhere: RCSB PDB 4LLS · PDBe 4LLS · UniProt Q16CN9
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