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Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc
Analyse Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0H
- Type
- protein
- Length
- 335 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217…
- Molecule
- UDP-glucose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- E8MF10
- Ligands
- NAD, UD1, MG
- Pockets
- 1 · best druggability 0.86
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-glucose 4-epimerase (EC 5.1.3.2) | protein | 335 | 41% helix, 19% strand | E8MF10 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.86 | 0.90 | 79 | NAD, UD1 |
Compared structures
- 6K0H · Crystal structure of udp-glucose 4-epimerase from bifidobacterium longum in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- E8MF10 · AlphaFold monomer V2.0 prediction for udp-glucose 4-epimerase (E8MF10) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 E8MF10
- Elsewhere: RCSB PDB 6K0H · PDBe 6K0H · UniProt E8MF10
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