Research workbench
Probing the structure and mechanism of de-N-acetylase from aggregatibacter actinomycetemcomitans
Analyse Probing the structure and mechanism of de-N-acetylase from aggregatibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U10
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
- UniProt
- A5HJW8
- Ligands
- ZN, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase | protein | 264 | 34% helix, 23% strand | A5HJW8 |
| B | Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase | protein | 262 | 35% helix, 24% strand | A5HJW8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.76 | 0.86 | 64 | ZN, CL |
| 2 | 136 | 0.71 | 0.91 | 35 | ZN, CL |
| 3 | 88 | 0.62 | 0.89 | 19 | empty |
| 4 | 204 | 0.51 | 0.76 | 33 | empty |
| 5 | 54 | 0.41 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1789 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4U10 · Probing the structure and mechanism of de-N-acetylase from aggregatibacter… · 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 A5HJW8
- Elsewhere: RCSB PDB 4U10 · PDBe 4U10 · UniProt A5HJW8
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