MolNFT v1 · #135132 · protein
X-ray structure of wlara (tdp-fucose-3,4-ketoisomerase) from campylobacter jejuni
5TPV · Wlara, tdp-fucose-3,4-ketoisomerase: “X-ray structure of wlara (tdp-fucose-3,4-ketoisomerase) from campylobacter jejuni”. X-ray diffraction, 2 ligands (TYD, PO4), 4 pockets (best druggability 0.61). MolNFT v1 #135132 on GenesisL1…
- PDB
- 5TPV
- Type
- protein
- Length
- 404 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlara, tdp-fucose-3,4-ketoisomerase
- UniProt
- Q9ALS3
- Ligands
- TYD, PO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wlara, tdp-fucose-3,4-ketoisomerase | protein | 135 | 9% helix, 49% strand | Q9ALS3 |
| B | Wlara, tdp-fucose-3,4-ketoisomerase | protein | 138 | 12% helix, 48% strand | Q9ALS3 |
| C | Wlara, tdp-fucose-3,4-ketoisomerase | protein | 131 | 8% helix, 45% strand | Q9ALS3 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.61 | 0.84 | 28 | TYD |
| 2 | 152 | 0.59 | 0.83 | 23 | TYD |
| 3 | 332 | 0.55 | 0.75 | 38 | empty |
| 4 | 58 | 0.38 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1846 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5TPV · X-ray structure of WlaRA (TDP-fucose-3,4-ketoisomerase) from Campylobacter jejuni · the same entry in another collection · chain B against B, 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 Q9ALS3
- Elsewhere: RCSB PDB 5TPV · PDBe 5TPV · UniProt Q9ALS3
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