MolNFT v1 · #98845 · protein
Crystal structure of a farnesyl diphosphate synthase from roseobacter denitrificans och 114, target efi-509393, with two ipp and calcium bound in active site
4LLT · Geranyltranstransferase: “Crystal structure of a farnesyl diphosphate synthase from roseobacter denitrificans och 114, target…”. X-ray diffraction, 2 ligands (IPE, CA), 5 pockets (best druggability 0.82). MolNFT v1 #98845 on…
- PDB
- 4LLT
- 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, CA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% 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 · 4 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.82 | 0.90 | 48 | IPE, CA |
| 2 | 511 | 0.80 | 0.87 | 69 | IPE, CA |
| 3 | 170 | 0.46 | 0.76 | 25 | empty |
| 4 | 142 | 0.42 | 0.75 | 25 | empty |
| 5 | 53 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1877 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4LLT · 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 4LLT · PDBe 4LLT · UniProt Q16CN9
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