MolNFT v1 · #139361 · protein
Homoserine dehydrogenase from thermus thermophilus HB8 complexed with hse
5XDF: “Homoserine dehydrogenase from thermus thermophilus HB8 complexed with hse”. X-ray diffraction, 2 ligands (HSE, NA), 4 pockets (best druggability 0.74). MolNFT v1 #139361 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XDF
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- Q5SL04
- Ligands
- HSE, NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 323 | 40% helix, 24% strand | Q5SL04 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 330 | 39% helix, 24% strand | Q5SL04 |
Ligands and binding sites
- HSE · L-homoserine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.74 | 0.88 | 53 | empty |
| 2 | 262 | 0.64 | 0.82 | 41 | HSE |
| 3 | 274 | 0.62 | 0.80 | 45 | HSE, FMT |
| 4 | 301 | 0.57 | 0.77 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 1728 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5XDF · Homoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE · 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 5XDF · PDBe 5XDF · UniProt Q5SL04
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