MolNFT v1 · #116692 · protein
Crystal structure of a udp-N-acetylglucosamine 2-epimerase from burkholderia vietnamiensis complexed with udp-glcnac and udp
5DLD: “Crystal structure of a udp-N-acetylglucosamine 2-epimerase from burkholderia vietnamiensis complexed with…”. X-ray diffraction, 3 ligands (UDP, UD1, NA), 1 pocket (best druggability 0.82). MolNFT v1 #116692 on GenesisL1: 3D…
- PDB
- 5DLD
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.