Research workbench
Structure of heparinase II complexed with heparan sulfate degradation disaccharide product
Analyse Structure of heparinase II complexed with heparan sulfate degradation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E80
- Type
- protein
- Length
- 2,241 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparinase II protein
- UniProt
- Q46080
- Ligands
- GCD, MAN, GCU, XYS, RAM, NDG, ZN, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Heparinase II protein | protein | 747 | 29% helix, 26% strand | Q46080 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 3 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B, C
- GCU · alpha-D-glucopyranuronic acid · sugar · 3 copies · chains A, B, C
- XYS · alpha-D-xylopyranose · sugar · 3 copies
- RAM · alpha-L-rhamnopyranose · sugar · 3 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.75 | 0.79 | 81 | empty |
| 2 | 712 | 0.72 | 0.78 | 69 | NDG, GCD, PO4 |
| 3 | 475 | 0.69 | 0.80 | 55 | empty |
| 4 | 464 | 0.69 | 0.80 | 56 | PO4 |
| 5 | 479 | 0.65 | 0.77 | 47 | PO4 |
Interfaces
2 interfaces between chains.
- B–C · 1439 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 3 modified (O-glycosylation, cyclization).
Compared structures
- 3E80 · Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product · 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 Q46080
- Elsewhere: RCSB PDB 3E80 · PDBe 3E80 · UniProt Q46080
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.