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Crystal structure of NAD+-bound xylitol dehydrogenase
Analyse Crystal structure of NAD+-bound xylitol dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZEM
- Type
- protein
- Length
- 2,080 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylitol dehydrogenase
- EC
- 1.1.1.9
- UniProt
- Q8GR61
- Ligands
- NAD, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Xylitol dehydrogenase (EC 1.1.1.9) | protein | 260 | 52% helix, 16% strand | Q8GR61 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 5 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.85 | 0.85 | 110 | NAD |
| 2 | 1112 | 0.85 | 0.85 | 110 | NAD |
| 3 | 979 | 0.84 | 0.85 | 103 | NAD |
| 4 | 1053 | 0.84 | 0.85 | 110 | NAD |
| 5 | 449 | 0.72 | 0.82 | 72 | MG |
Interfaces
13 interfaces between chains.
- B–D · 1775 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 1771 Ų buried · 25 hydrogen bonds · protein-protein
- F–H · 1766 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1759 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1193 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1ZEM · Crystal Structure of NAD+-Bound Xylitol Dehydrogenase · 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 Q8GR61
- Elsewhere: RCSB PDB 1ZEM · PDBe 1ZEM · UniProt Q8GR61
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