MolNFT v1 · #17006 · protein
Crystal structure of chondroitinase B complexed to chondroitin 4- sulfate tetrasaccharide
1OFM: “Crystal structure of chondroitinase B complexed to chondroitin 4- sulfate tetrasaccharide”. X-ray diffraction, 10 ligands (ASG, MXZ, GCD), 3 pockets (best druggability 0.50). MolNFT v1 #17006 on GenesisL1: 3D structure, binding…
- PDB
- 1OFM
- Type
- protein
- Length
- 481 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chondroitinase B
- EC
- 4.2.2.4
- UniProt
- Q46079
- Ligands
- ASG, MXZ, GCD, MAN, GCU, XYP, GLA, BGC, RAM, BDP
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitinase B (EC 4.2.2.4) | protein | 481 | 11% helix, 31% strand | Q46079 |
Ligands and binding sites
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains A
- MXZ · 2-O-methyl-alpha-L-fucopyranose · ligand
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand
- MAN · alpha-D-mannopyranose · sugar · chains A
- GCU · alpha-D-glucopyranuronic acid · sugar · chains A
- XYP · beta-D-xylopyranose · sugar
- GLA · alpha-D-galactopyranose · sugar
- BGC · beta-D-glucopyranose · sugar
- RAM · alpha-L-rhamnopyranose · sugar · chains A
- BDP · beta-D-glucopyranuronic acid · 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 | 205 | 0.50 | 0.76 | 40 | ASG |
| 2 | 60 | 0.35 | 0.78 | 16 | empty |
| 3 | 52 | 0.26 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 1 glycan, 1 modified (O-glycosylation, cyclization).
Compared structures
- 1OFM · Crystal structure of chondroitinase B complexed to chondroitin 4-sulfate tetrasaccharide · the same entry in another collection · chain A against A, TM-score 1.00
- Q46079 · AlphaFold monomer V2.0 prediction for chondroitinase-B (Q46079) · a predicted model of the same protein · 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 Q46079
- Elsewhere: RCSB PDB 1OFM · PDBe 1OFM · UniProt Q46079
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