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L-threonine dehydrogenase (tktdh) from the hyperthermophilic archaeon thermococcus kodakaraensis
Analyse L-threonine dehydrogenase (tktdh) from the hyperthermophilic archaeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GFB
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase
- EC
- 1.1.1.103
- UniProt
- Q5JI69
- Ligands
- NAD, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 347 | 31% helix, 28% strand | Q5JI69 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.73 | 0.79 | 60 | NAD |
| 2 | 696 | 0.72 | 0.78 | 59 | NAD |
| 3 | 712 | 0.69 | 0.76 | 64 | NAD |
| 4 | 667 | 0.69 | 0.77 | 57 | NAD |
| 5 | 219 | 0.68 | 0.85 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1670 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1641 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 706 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3GFB · L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus… · the same entry in another collection · chain C against C, TM-score 1.00
- Q5JI69 · AlphaFold monomer V2.0 prediction for L-threonine 3-dehydrogenase (Q5JI69) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5JI69
- Elsewhere: RCSB PDB 3GFB · PDBe 3GFB · UniProt Q5JI69
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