Research workbench
High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.
Analyse High-resolution crystal structures of N-Acetylmannosamine kinase: Insights… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YHW
- Type
- protein
- Length
- 309 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.64
- Source
- HOMO SAPIENS
- Molecule
- Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N-acetylmannosamine kinase
- EC
- 2.7.1.60
- UniProt
- Q9Y223
- Ligands
- BM3, ZN, CA, CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.64 · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N-acetylmannosamine kinase (EC 2.7.1.60) | protein | 309 | 40% helix, 25% strand | Q9Y223 |
Ligands and binding sites
- BM3 · 2-acetamido-2-deoxy-alpha-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- 2PE · Nonaethylene glycol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.65 | 0.81 | 49 | BM3 |
| 2 | 75 | 0.35 | 0.76 | 13 | empty |
| 3 | 66 | 0.32 | 0.75 | 13 | empty |
| 4 | 50 | 0.25 | 0.73 | 16 | PGE |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2YHW · High-resolution crystal structures of N-acetylmannosamine kinase: insights about… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y223 · AlphaFold monomer V2.0 prediction for bifunctional udp-N- acetylglucosamine… · a predicted model of the same protein · 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 Q9Y223
- Elsewhere: RCSB PDB 2YHW · PDBe 2YHW · UniProt Q9Y223
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.