Research workbench
Structure of thermoplasma acidophilum aldohexose dehydrogenase (aldt) in ligand-free form
Analyse Structure of thermoplasma acidophilum aldohexose dehydrogenase (aldt) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DTD
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase related protein
- EC
- 1.1.1.118
- UniProt
- Q9HK51
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose 1-dehydrogenase related protein (EC 1.1.1.118) | protein | 255 | 48% helix, 15% strand | Q9HK51 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 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 | 706 | 0.77 | 0.82 | 57 | SO4 |
| 2 | 607 | 0.75 | 0.81 | 54 | SO4 |
| 3 | 99 | 0.38 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1788 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DTD · Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form · 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 Q9HK51
- Elsewhere: RCSB PDB 2DTD · PDBe 2DTD · UniProt Q9HK51
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