MolNFT v1 · #114312 · protein
X-ray structure of the pglf udp-N-acetylglucosamine 4,6-dehydratase from campylobacterjejuni, D396N/K397A variant in complex with udp-N- acrtylglucosamine
5BJV · Wlal protein: “X-ray structure of the pglf udp-N-acetylglucosamine 4,6-dehydratase from campylobacterjejuni, D396N/K397A…”. X-ray diffraction, 3 ligands (NAD, UD1, NA), 8 pockets (best druggability 0.86). MolNFT v1 #114312 on…
- PDB
- 5BJV
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlal protein
- UniProt
- O86159
- Ligands
- NAD, UD1, NA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wlal protein | protein | 339 | 45% helix, 17% strand | O86159 |
| B | Wlal protein | protein | 338 | 45% helix, 17% strand | O86159 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.86 | 0.87 | 87 | NAD, UD1 |
| 2 | 859 | 0.85 | 0.88 | 84 | NAD, UD1, EDO |
| 3 | 210 | 0.57 | 0.80 | 30 | empty |
| 4 | 122 | 0.45 | 0.78 | 18 | empty |
| 5 | 125 | 0.41 | 0.75 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5BJV · X-ray structure of the PglF UDP-N-acetylglucosamine 4,6-dehydratase from… · 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 O86159
- Elsewhere: RCSB PDB 5BJV · PDBe 5BJV · UniProt O86159
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