MolNFT v1 · #35721 · protein
Homoserine dehydrogenase from thermus thermophilus HB8
2EJW: “Homoserine dehydrogenase from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (MG, NO3), 11 pockets (best druggability 0.84). MolNFT v1 #35721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2EJW
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- Q5SL04
- Ligands
- MG, NO3
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 331 | 39% helix, 23% strand | Q5SL04 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, E, F
- NO3 · Nitrate ion · ion · 3 copies · chains A, E, F
- GOL · Glycerol · additive · 2 copies · chains B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.84 | 0.85 | 122 | NO3 |
| 2 | 325 | 0.81 | 0.91 | 73 | MG |
| 3 | 218 | 0.78 | 0.92 | 47 | GOL |
| 4 | 503 | 0.65 | 0.77 | 63 | NO3 |
| 5 | 367 | 0.64 | 0.79 | 39 | NO3 |
Interfaces
3 interfaces between chains.
- E–F · 1965 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1896 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 1330 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2EJW · Homoserine Dehydrogenase from Thermus thermophilus HB8 · 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 Q5SL04
- Elsewhere: RCSB PDB 2EJW · PDBe 2EJW · UniProt Q5SL04
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