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Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP
Analyse Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DLD
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Burkholderia vietnamiensis
- Molecule
- UDP-N-Acetylglucosamine 2-epimerase
- EC
- 5.1.3.14
- UniProt
- A4JLG9
- Ligands
- UDP, UD1, NA
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.45 · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-N-Acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 379 | 49% helix, 15% strand | A4JLG9 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · 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 | 400 | 0.82 | 0.91 | 58 | UDP, UD1, ACT |
Compared structures
- 5DLD · Crystal structure of a udp-N-acetylglucosamine 2-epimerase from burkholderia… · 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 A4JLG9
- Elsewhere: RCSB PDB 5DLD · PDBe 5DLD · UniProt A4JLG9
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