MolNFT v1 · #151736 · protein
Glucosamine kinase in complex with glucosamine, ADP and inorganic phosphate
6HWL: “Glucosamine kinase in complex with glucosamine, ADP and inorganic phosphate”. X-ray diffraction, 5 ligands (ADP, GCS, MG), 10 pockets (best druggability 0.74). MolNFT v1 #151736 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6HWL
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine kinase
- UniProt
- A0A1H7TQR5
- Ligands
- ADP, GCS, MG, CL, PO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine kinase | protein | 420 | 47% helix, 19% strand | A0A1H7TQR5 |
| B | Glucosamine kinase | protein | 397 | 51% helix, 18% strand | A0A1H7TQR5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.74 | 0.77 | 83 | empty |
| 2 | 483 | 0.70 | 0.80 | 57 | ADP, MG, PO4 |
| 3 | 480 | 0.69 | 0.80 | 49 | empty |
| 4 | 181 | 0.69 | 0.87 | 22 | PEG |
| 5 | 390 | 0.68 | 0.81 | 40 | GCS |
Interfaces
1 interface between chains.
- A–B · 224 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HWL · Glucosamine kinase in complex with glucosamine, ADP and inorganic phosphate · 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 A0A1H7TQR5
- Elsewhere: RCSB PDB 6HWL · PDBe 6HWL · UniProt A0A1H7TQR5
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