MolNFT v1 · #68767 · protein
Crystal structure of a carbohydrate kinase (yjef FAMILY)FROM helicobacter pylori
3K5W: “Crystal structure of a carbohydrate kinase (yjef FAMILY)FROM helicobacter pylori”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.64). MolNFT v1 #68767 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3K5W
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate kinase
- UniProt
- P56176
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate kinase | protein | 461 | 37% helix, 21% strand | P56176 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.64 | 0.82 | 37 | PO4 |
| 2 | 102 | 0.62 | 0.88 | 19 | empty |
| 3 | 164 | 0.52 | 0.79 | 31 | empty |
| 4 | 77 | 0.37 | 0.76 | 15 | empty |
| 5 | 100 | 0.37 | 0.75 | 25 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3K5W · Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- P56176 · AlphaFold monomer V2.0 prediction for bifunctional NAD(P)H-hydrate repair enzyme nnr… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P56176
- Elsewhere: RCSB PDB 3K5W · PDBe 3K5W · UniProt P56176
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