Research workbench
Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 ångströms
Analyse Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K50
- Type
- protein
- Length
- 1,914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase
- EC
- 1.1.1.103
- UniProt
- Q7YW97
- Ligands
- NAD, ALO
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, J | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 319 | 46% helix, 16% strand | Q7YW97 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, C, E, G, I, J
- ALO · Allo-threonine · ligand · 2 copies · chains C, G
- GOL · Glycerol · additive · 8 copies · chains A, E, G, I, J
- ACT · Acetate ion · additive · 4 copies · chains A, C, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.79 | 0.84 | 71 | NAD, ALO |
| 2 | 364 | 0.75 | 0.86 | 45 | NAD, GOL |
| 3 | 349 | 0.74 | 0.85 | 49 | NAD, GOL |
| 4 | 302 | 0.73 | 0.86 | 49 | ACT |
| 5 | 416 | 0.72 | 0.83 | 64 | empty |
Interfaces
6 interfaces between chains.
- C–G · 1297 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1261 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 408 Ų buried · 3 hydrogen bonds · protein-protein
- G–I · 260 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 76 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5K50 · Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound… · 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 Q7YW97
- Elsewhere: RCSB PDB 5K50 · PDBe 5K50 · UniProt Q7YW97
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.