Research workbench
Cryo-EM structure of human HGSNAT in inactive state
Analyse Cryo-EM structure of human HGSNAT in inactive state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8VLV
- Type
- protein
- Length
- 1,085 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.49
- Source
- Homo sapiens
- Molecule
- Heparan-alpha-glucosaminide N-acetyltransferase
- EC
- 2.3.1.78
- UniProt
- Q68CP4
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.78
Structure
electron microscopy · resolution 3.49 · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparan-alpha-glucosaminide N-acetyltransferase (EC 2.3.1.78) | protein | 542 | 48% helix, 10% strand | Q68CP4 |
| B | Heparan-alpha-glucosaminide N-acetyltransferase (EC 2.3.1.78) | protein | 543 | 48% helix, 10% strand | Q68CP4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.78 | 0.81 | 57 | empty |
| 2 | 1026 | 0.75 | 0.78 | 103 | empty |
| 3 | 788 | 0.72 | 0.77 | 76 | empty |
| 4 | 158 | 0.60 | 0.83 | 27 | empty |
| 5 | 226 | 0.57 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1393 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- Q68CP4 · AlphaFold monomer V2.0 prediction for heparan-alpha-glucosaminide N-acetyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q68CP4
- Elsewhere: RCSB PDB 8VLV · PDBe 8VLV · UniProt Q68CP4
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