Research workbench
X-ray structure of a glucosamine N-acetyltransferase from clostridium acetobutylicum in complex with chitosan
Analyse X-ray structure of a glucosamine N-acetyltransferase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KGP
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted acetyltransferase
- UniProt
- Q97ML2
- Ligands
- COA, PA1, ACO, GCS
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Predicted acetyltransferase | protein | 316 | 35% helix, 32% strand | Q97ML2 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, B
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, B
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.79 | 0.86 | 48 | ACO |
| 2 | 474 | 0.78 | 0.85 | 48 | ACO, EDO |
| 3 | 481 | 0.69 | 0.80 | 64 | PA1, GCS, COA, MPO |
| 4 | 469 | 0.67 | 0.79 | 59 | PA1, GCS, COA |
| 5 | 114 | 0.64 | 0.88 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1450 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5KGP · X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in… · the same entry in another collection · chain B against B, 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 Q97ML2
- Elsewhere: RCSB PDB 5KGP · PDBe 5KGP · UniProt Q97ML2
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