Research workbench
Crystal structure of AGD3 a novel carbohydrate deacetylase
Analyse Crystal structure of AGD3 a novel carbohydrate deacetylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NWZ
- Type
- protein
- Length
- 665 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate deacetylase AGD3
- UniProt
- Q4WX15
- Ligands
- NAG, MAN, ZN, CL
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate deacetylase AGD3 | protein | 665 | 30% helix, 24% strand | Q4WX15 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 6 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.58 | 0.83 | 31 | empty |
| 2 | 213 | 0.51 | 0.76 | 37 | ZN |
| 3 | 116 | 0.43 | 0.77 | 20 | empty |
| 4 | 146 | 0.42 | 0.75 | 23 | empty |
| 5 | 134 | 0.39 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 4 glycan, 3 disulfide (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 6NWZ · Crystal structure of Agd3 a novel carbohydrate deacetylase · 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 Q4WX15
- Elsewhere: RCSB PDB 6NWZ · PDBe 6NWZ · UniProt Q4WX15
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