MolNFT v1 · #55358 · protein
Structure of N-acetylmannosamine kinase in complex with N- acetylmannosamine and ADP
2YHY · Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N…: “Structure of N-acetylmannosamine kinase in complex with N- acetylmannosamine and ADP”. X-ray diffraction, 6 ligands (BM3, ADP, CA), 3 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 2YHY
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase
- EC
- 2.7.1.60
- UniProt
- Q9Y223
- Ligands
- BM3, ADP, CA, MG, ZN, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 308 | 41% helix, 25% strand | Q9Y223 |
Ligands and binding sites
- BM3 · 2-acetamido-2-deoxy-alpha-D-mannopyranose · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
- 2PE · Nonaethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.67 | 0.82 | 50 | BM3, MG, ADP |
| 2 | 63 | 0.34 | 0.76 | 12 | empty |
| 3 | 70 | 0.33 | 0.75 | 11 | empty |
Compared structures
- 2YHY · Structure of N-Acetylmannosamine kinase in complex with N- acetylmannosamine and ADP · 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 2YHY · PDBe 2YHY · UniProt Q9Y223
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