MolNFT v1 · #55888 · protein
Crystal structure of thermolabile L-threonine dehydrogenase from flavobacterium frigidimaris kuc-1
2YY7: “Crystal structure of thermolabile L-threonine dehydrogenase from flavobacterium frigidimaris kuc-1”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.75). MolNFT v1 #55888 on GenesisL1: 3D structure, binding sites…
- PDB
- 2YY7
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine dehydrogenase
- EC
- 1.1.1.103
- UniProt
- Q8KZM4
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-threonine dehydrogenase (EC 1.1.1.103) | protein | 312 | 45% helix, 16% strand | Q8KZM4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.75 | 0.86 | 42 | NAD, GOL |
| 2 | 337 | 0.73 | 0.85 | 43 | NAD, GOL |
| 3 | 147 | 0.43 | 0.74 | 27 | PE8 |
| 4 | 81 | 0.33 | 0.75 | 21 | empty |
| 5 | 74 | 0.31 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2YY7 · Crystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium… · 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 Q8KZM4
- Elsewhere: RCSB PDB 2YY7 · PDBe 2YY7 · UniProt Q8KZM4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.