Research workbench
The crystal structure of human transhydrogenase domain III with bound NADP
Analyse The crystal structure of human transhydrogenase domain III with bound NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJL
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Transhydrogenase diii
- EC
- 1.6.1.1
- UniProt
- Q13423
- Ligands
- NAP, SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transhydrogenase diii (EC 1.6.1.1) | protein | 182 | 42% helix, 18% strand | Q13423 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.57 | 0.79 | 32 | NAP, GOL |
| 2 | 212 | 0.55 | 0.78 | 33 | NAP, GOL |
| 3 | 205 | 0.46 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1DJL · The crystal structure of human transhydrogenase domain III with bound NADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q13423 · AlphaFold monomer V2.0 prediction for NAD(P) transhydrogenase, mitochondrial (Q13423) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q13423
- Elsewhere: RCSB PDB 1DJL · PDBe 1DJL · UniProt Q13423
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