MolNFT v1 · #83480 · protein
Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with farnesyl S-thiol-pyrophosphate (fspp)
3WJN · Octaprenyl diphosphate synthase: “Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with farnesyl…”. X-ray diffraction, 1 ligand (FPS), 3 pockets (best druggability 0.78). MolNFT v1 #83480 on GenesisL1: 3D…
- PDB
- 3WJN
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octaprenyl diphosphate synthase
- EC
- 2.5.1.-
- UniProt
- K0BUH0
- Ligands
- FPS
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octaprenyl diphosphate synthase (EC 2.5.1.-) | protein | 306 | 75% helix, 0% strand | K0BUH0 |
| B | Octaprenyl diphosphate synthase (EC 2.5.1.-) | protein | 302 | 77% helix, 0% strand | K0BUH0 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.78 | 0.81 | 78 | FPS |
| 2 | 646 | 0.69 | 0.77 | 70 | empty |
| 3 | 94 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1781 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3WJN · Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli with… · 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 K0BUH0
- Elsewhere: RCSB PDB 3WJN · PDBe 3WJN · UniProt K0BUH0
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