Research workbench
X-ray structure of human N-acetyl galactosamine kinase complexed with mg-ADP and N-acetyl galactosamine 1-phosphate
Analyse X-ray structure of human N-acetyl galactosamine kinase complexed with mg-ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A2C
- Type
- protein
- Length
- 446 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylgalactosamine kinase
- EC
- 2.7.1.-
- UniProt
- Q01415
- Ligands
- NG1, ADP, MG, NA, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylgalactosamine kinase (EC 2.7.1.-) | protein | 446 | 46% helix, 20% strand | Q01415 |
Ligands and binding sites
- NG1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.79 | 0.90 | 51 | NG1, MG, ADP |
| 2 | 147 | 0.42 | 0.75 | 24 | empty |
| 3 | 115 | 0.41 | 0.76 | 20 | empty |
| 4 | 60 | 0.39 | 0.79 | 16 | empty |
| 5 | 52 | 0.27 | 0.75 | 19 | empty |
Compared structures
- 2A2C · x-ray structure of human N-acetyl galactosamine kinase complexed with Mg-ADP and N-acetyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01415 · AlphaFold monomer V2.0 prediction for N-acetylgalactosamine kinase (Q01415) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q01415
- Elsewhere: RCSB PDB 2A2C · PDBe 2A2C · UniProt Q01415
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