Research workbench
X-ray structure of the pglf 4,6-dehydratase from campylobacter jejuni, T595S variant, in complex with udp
Analyse X-ray structure of the pglf 4,6-dehydratase from campylobacter jejuni, T595S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BJW
- Type
- protein
- Length
- 679 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
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wlal protein | protein | 340 | 45% helix, 18% strand | O86159 |
| 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 · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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 | 1000 | 0.85 | 0.85 | 87 | NA, NAD, UDP, EDO |
| 2 | 989 | 0.84 | 0.85 | 86 | UDP, NAD, EDO, NA |
| 3 | 209 | 0.60 | 0.81 | 29 | empty |
| 4 | 117 | 0.44 | 0.77 | 18 | empty |
| 5 | 129 | 0.42 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1272 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5BJW · X-ray structure of the PglF 4,6-dehydratase from campylobacter jejuni, T595S variant, 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 5BJW · PDBe 5BJW · UniProt O86159
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.