MolNFT v1 · #125547 · protein
L-threonine dehydrogenase from trypanosoma brucei with NAD and the inhibitor pyruvate bound.
5LC1 · L-threonine 3-dehydrogenase: “L-threonine dehydrogenase from trypanosoma brucei with NAD and the inhibitor pyruvate bound.”. X-ray diffraction, 3 ligands (NAD, PYR, NA), 11 pockets (best druggability 0.76). MolNFT v1 #125547 on…
- PDB
- 5LC1
- Type
- protein
- Length
- 1,920 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, PYR, NA
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 320 | 46% helix, 15% strand | Q7YW97 |
| B | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 321 | 46% helix, 15% strand | Q7YW97 |
| F | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 319 | 46% helix, 15% strand | Q7YW97 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- PYR · Pyruvic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 3 copies · chains A, B, E
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.76 | 0.86 | 44 | NAD, PYR |
| 2 | 328 | 0.74 | 0.86 | 49 | NAD, PYR |
| 3 | 410 | 0.74 | 0.84 | 56 | NAD, PYR |
| 4 | 308 | 0.74 | 0.86 | 46 | NAD, PYR |
| 5 | 326 | 0.74 | 0.85 | 47 | NAD, PYR |
Interfaces
2 interfaces between chains.
- A–F · 279 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5LC1 · L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate… · 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 5LC1 · PDBe 5LC1 · UniProt Q7YW97
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