Research workbench
Homoserine dehydrogenase from thermus thermophilus HB8 complexed with hse and NADPH
Analyse Homoserine dehydrogenase from thermus thermophilus HB8 complexed with hse and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A0S
- Type
- protein
- Length
- 662 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, NDP, NA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 331 | 39% helix, 24% strand | Q5SL04 |
Ligands and binding sites
- HSE · L-homoserine · ligand · 2 copies · chains B, A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains B, A
- NA · Sodium ion · metal · 2 copies · chains B, A
- FMT · Formic acid · additive · 13 copies · chains B, A
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains B
- GOL · Glycerol · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.74 | 0.89 | 49 | empty |
| 2 | 331 | 0.65 | 0.80 | 46 | HSE, NDP |
| 3 | 312 | 0.63 | 0.80 | 45 | HSE, NDP |
| 4 | 64 | 0.58 | 0.89 | 26 | FMT |
| 5 | 136 | 0.46 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 1964 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6A0S · Homoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE and NADPH · 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 6A0S · PDBe 6A0S · UniProt Q5SL04
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