Research workbench
Crystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine
Analyse Crystal structure of human N-acetylglucosamine kinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CH5
- Type
- protein
- Length
- 1,370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nagk protein
- EC
- 2.7.1.59
- UniProt
- Q6IA84
- Ligands
- NAG, NDG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nagk protein (EC 2.7.1.59) | protein | 344 | 45% helix, 21% strand | Q6IA84 |
| B, D | Nagk protein (EC 2.7.1.59) | protein | 342 | 46% helix, 21% strand | Q6IA84 |
| C | Nagk protein (EC 2.7.1.59) | protein | 342 | 44% helix, 21% strand | Q6IA84 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.82 | 0.83 | 131 | NAG, GOL, NDG |
| 2 | 1093 | 0.81 | 0.82 | 144 | NAG, GOL |
| 3 | 675 | 0.73 | 0.79 | 47 | empty |
| 4 | 670 | 0.73 | 0.80 | 47 | empty |
| 5 | 274 | 0.66 | 0.82 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1898 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1883 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 512 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2CH5 · Crystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine · the same entry in another collection · 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 Q6IA84
- Elsewhere: RCSB PDB 2CH5 · PDBe 2CH5 · UniProt Q6IA84
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