MolNFT v1 · #34428 · protein
Hyperthermophilic threonine dehydrogenase from pyrococcus horikoshii
2DFV · Probable L-threonine 3-dehydrogenase: “Hyperthermophilic threonine dehydrogenase from pyrococcus horikoshii”. X-ray diffraction, 3 ligands (NAD, ZN, SO4), 7 pockets (best druggability 0.67). MolNFT v1 #34428 on GenesisL1: 3D…
- PDB
- 2DFV
- Type
- protein
- Length
- 1,038 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable L-threonine 3-dehydrogenase
- EC
- 1.1.1.103
- UniProt
- O58389
- Ligands
- NAD, ZN, SO4
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 346 | 30% helix, 27% strand | O58389 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.67 | 0.77 | 54 | SO4, NAD |
| 2 | 555 | 0.67 | 0.77 | 52 | SO4, NAD |
| 3 | 574 | 0.66 | 0.76 | 50 | SO4, NAD |
| 4 | 189 | 0.54 | 0.79 | 39 | empty |
| 5 | 154 | 0.45 | 0.76 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–C · 826 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2DFV · Hyperthermophilic threonine dehydrogenase from Pyrococcus horikoshii · the same entry in another collection · chain B against B, TM-score 1.00
- O58389 · AlphaFold monomer V2.0 prediction for L-threonine 3-dehydrogenase (O58389) · a predicted model of the same protein · 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 O58389
- Elsewhere: RCSB PDB 2DFV · PDBe 2DFV · UniProt O58389
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