Research workbench
Crystal structure of chondroitinase B
Analyse Crystal structure of chondroitinase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DBO
- Type
- protein
- Length
- 481 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chondroitinase B
- Ligands
- MXY, G4D, ASG, GC4, MAN, GCU, XYP, BGC, RAM
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitinase B | protein | 481 | 11% helix, 32% strand | — |
Ligands and binding sites
- MXY · 2-O-methyl-beta-L-fucopyranose · ligand
- G4D · 4-deoxy-alpha-D-glucopyranose · ligand
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · ligand · chains A
- GC4 · 4-deoxy-beta-D-glucopyranuronic acid · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- GCU · alpha-D-glucopyranuronic acid · sugar · chains A
- XYP · beta-D-xylopyranose · sugar
- BGC · beta-D-glucopyranose · sugar
- RAM · alpha-L-rhamnopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.48 | 0.75 | 40 | ASG |
| 2 | 54 | 0.30 | 0.76 | 13 | empty |
| 3 | 55 | 0.27 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 1DBO · Crystal structure of chondroitinase B · 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
- Elsewhere: RCSB PDB 1DBO · PDBe 1DBO
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