MolNFT v1 · #124086 · protein
Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma brucei refined to 1.77 ångströms
5K4Y: “Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma brucei refined to 1.77 ångströms”. X-ray diffraction, 3 ligands (NAD, NA, CL), 12 pockets (best druggability 0.73). MolNFT v1 #124086 on GenesisL1: 3D…
- PDB
- 5K4Y
- Type
- protein
- Length
- 1,919 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, NA, CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 320 | 47% helix, 15% strand | Q7YW97 |
| E | 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
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.73 | 0.82 | 47 | NAD, ACT, CL, NA |
| 2 | 574 | 0.73 | 0.80 | 56 | NAD, ACT, CL, NA |
| 3 | 523 | 0.72 | 0.81 | 53 | NAD, ACT, CL, NA |
| 4 | 420 | 0.72 | 0.82 | 45 | NAD, ACT, CL, NA |
| 5 | 517 | 0.72 | 0.80 | 51 | NAD, ACT, CL, NA |
Interfaces
2 interfaces between chains.
- A–F · 244 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5K4Y · Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei… · 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 5K4Y · PDBe 5K4Y · UniProt Q7YW97
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