MolNFT v1 · #81124 · protein
Crystal structure of saccharopine dehydrogenase from saccharomyces cervisiae complexed with NAD.
3UHA · Saccharopine dehydrogenase [NAD+, L-lysine-forming]: “Crystal structure of saccharopine dehydrogenase from saccharomyces cervisiae complexed with NAD.”. X-ray diffraction, 2 ligands (NAD, CL), 6 pockets (best druggability 0.68).…
- PDB
- 3UHA
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saccharopine dehydrogenase [NAD+, L-lysine-forming]
- EC
- 1.5.1.7
- UniProt
- P38998
- Ligands
- NAD, CL
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) | protein | 365 | 37% helix, 14% strand | P38998 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.68 | 0.77 | 51 | empty |
| 2 | 599 | 0.66 | 0.76 | 52 | NAD |
| 3 | 595 | 0.65 | 0.76 | 52 | NAD |
| 4 | 555 | 0.65 | 0.76 | 52 | empty |
| 5 | 111 | 0.48 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UHA · Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P38998 · AlphaFold monomer V2.0 prediction for saccharopine dehydrogenase [NAD(+)… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P38998
- Elsewhere: RCSB PDB 3UHA · PDBe 3UHA · UniProt P38998
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