MolNFT v1 · #83481 · protein
Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with isopentenyl pyrophosphate (ipp)
3WJO · Octaprenyl diphosphate synthase: “Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with isopentenyl pyrophosphate…”. X-ray diffraction, 1 ligand (IPE), 3 pockets (best druggability 0.78). MolNFT v1 #83481…
- PDB
- 3WJO
- 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
- IPE
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octaprenyl diphosphate synthase (EC 2.5.1.-) | protein | 302 | 74% helix, 1% strand | K0BUH0 |
| B | Octaprenyl diphosphate synthase (EC 2.5.1.-) | protein | 306 | 76% helix, 0% strand | K0BUH0 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.78 | 0.81 | 81 | IPE |
| 2 | 586 | 0.67 | 0.77 | 67 | empty |
| 3 | 75 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1780 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3WJO · 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 3WJO · PDBe 3WJO · UniProt K0BUH0
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