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Active site of chondroitinase ac lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis
Analyse Active site of chondroitinase ac lyase revealed by the structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HM3
- Type
- protein
- Length
- 674 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chondroitinase ac
- EC
- 4.2.2.5
- UniProt
- Q59288
- Ligands
- MXY, MAN, GCU, RAM, XYP, NAG, BDP, CA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitinase ac (EC 4.2.2.5) | protein | 674 | 31% helix, 29% strand | Q59288 |
Ligands and binding sites
- MXY · 2-O-methyl-beta-L-fucopyranose · ligand
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- GCU · alpha-D-glucopyranuronic acid · sugar · 2 copies · chains A
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A
- XYP · beta-D-xylopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- BDP · beta-D-glucopyranuronic acid · sugar · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.62 | 0.74 | 63 | NAG, BDP |
| 2 | 85 | 0.47 | 0.82 | 16 | empty |
| 3 | 55 | 0.31 | 0.76 | 15 | empty |
| 4 | 52 | 0.27 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
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 Q59288
- Elsewhere: RCSB PDB 1HM3 · PDBe 1HM3 · UniProt Q59288
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