Research workbench
Crystal structure of human N-acetylglucosamine kinase in complex with ADP and glucose
Analyse Crystal structure of human N-acetylglucosamine kinase in complex with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CH6
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-D-glucosamine kinase
- EC
- 2.7.1.59
- UniProt
- Q9UJ70
- Ligands
- ADP, GLC
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-acetyl-D-glucosamine kinase (EC 2.7.1.59) | protein | 343 | 45% helix, 20% strand | Q9UJ70 |
| B | N-acetyl-D-glucosamine kinase (EC 2.7.1.59) | protein | 310 | 41% helix, 16% strand | Q9UJ70 |
| C | N-acetyl-D-glucosamine kinase (EC 2.7.1.59) | protein | 337 | 44% helix, 21% strand | Q9UJ70 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.78 | 0.80 | 96 | ADP, GLC |
| 2 | 434 | 0.77 | 0.86 | 42 | empty |
| 3 | 770 | 0.77 | 0.81 | 80 | ADP, GLC |
| 4 | 960 | 0.74 | 0.77 | 82 | ADP, GLC |
| 5 | 675 | 0.73 | 0.79 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1718 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1683 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 743 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2CH6 · Crystal structure of human N-acetylglucosamine kinase in complex with ADP and glucose · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJ70 · AlphaFold monomer V2.0 prediction for N-acetyl-D-glucosamine kinase (Q9UJ70) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9UJ70
- Elsewhere: RCSB PDB 2CH6 · PDBe 2CH6 · UniProt Q9UJ70
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