MolNFT v1 · #142323 · protein
Homoserine dehydrogenase from thermus thermophilus HB8 unliganded form
6A0R: “Homoserine dehydrogenase from thermus thermophilus HB8 unliganded form”. X-ray diffraction, 2 ligands (UNL, NA), 5 pockets (best druggability 0.75). MolNFT v1 #142323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A0R
- Type
- protein
- Length
- 663 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
- UNL, NA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 331 | 39% helix, 23% strand | Q5SL04 |
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 332 | 39% helix, 23% strand | Q5SL04 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains B, A
- FMT · Formic acid · additive · 17 copies · chains B, A
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 2 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.75 | 0.91 | 40 | empty |
| 2 | 352 | 0.68 | 0.82 | 40 | FMT |
| 3 | 368 | 0.66 | 0.80 | 44 | FMT |
| 4 | 300 | 0.62 | 0.80 | 44 | CXS |
| 5 | 50 | 0.50 | 0.87 | 20 | FMT |
Interfaces
1 interface between chains.
- B–A · 1901 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6A0R · Homoserine dehydrogenase from Thermus thermophilus HB8 unliganded form · the same entry in another collection · chain B against B, 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 6A0R · PDBe 6A0R · UniProt Q5SL04
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