Research workbench
Crystal structure of herbaspirillum huttiense L-arabinose 1- dehydrogenase (NAD bound form)
Analyse Crystal structure of herbaspirillum huttiense L-arabinose 1- dehydrogenase (NAD… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WWX
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)-dependent dehydrogenase (short-subunit alcohol dehydrogenase family)
- UniProt
- A0A4R8JL46
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD(P)-dependent dehydrogenase (short-subunit alcohol dehydrogenase family) | protein | 254 | 53% helix, 16% strand | A0A4R8JL46 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.76 | 0.85 | 44 | NAD |
| 2 | 434 | 0.75 | 0.84 | 43 | NAD |
| 3 | 103 | 0.40 | 0.76 | 22 | empty |
| 4 | 105 | 0.39 | 0.76 | 19 | empty |
| 5 | 110 | 0.39 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1817 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7WWX · Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound 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 A0A4R8JL46
- Elsewhere: RCSB PDB 7WWX · PDBe 7WWX · UniProt A0A4R8JL46
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