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Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma brucei bound to NAD+ refined to 2.2 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
- 5K4V
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- 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, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 320 | 47% helix, 15% strand | Q7YW97 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- ACT · Acetate ion · additive · 8 copies · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.74 | 0.85 | 48 | NAD, ACT, NA |
| 2 | 343 | 0.73 | 0.84 | 50 | NAD, ACT, NA |
| 3 | 426 | 0.72 | 0.82 | 63 | GOL, ACT |
| 4 | 60 | 0.35 | 0.78 | 18 | empty |
| 5 | 57 | 0.33 | 0.77 | 13 | GOL |
Interfaces
1 interface between chains.
- A–C · 1243 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5K4V · 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 5K4V · PDBe 5K4V · UniProt Q7YW97
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