MolNFT v1 · #114315 · protein
X-ray structure of the pglf 4,5-dehydratase from campylobacter jejuni, variant M405Y, in complex with udp
5BJY · Wlal protein: “X-ray structure of the pglf 4,5-dehydratase from campylobacter jejuni, variant M405Y, in complex with udp”. X-ray diffraction, 3 ligands (UDP, NAD, NA), 7 pockets (best druggability 0.86). MolNFT v1 #114315 on…
- PDB
- 5BJY
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlal protein
- UniProt
- O86159
- Ligands
- UDP, NAD, NA
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wlal protein | protein | 339 | 45% helix, 18% strand | O86159 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.86 | 0.89 | 84 | UDP, NAD, EDO, NA |
| 2 | 830 | 0.86 | 0.88 | 82 | UDP, NAD, EDO |
| 3 | 220 | 0.59 | 0.80 | 32 | empty |
| 4 | 132 | 0.43 | 0.76 | 19 | empty |
| 5 | 133 | 0.42 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1246 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5BJY · x-ray structure of the PglF 4,5-dehydratase from campylobacter jejuni, variant M405Y, in… · 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 5BJY · PDBe 5BJY · UniProt O86159
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