Research workbench
Crystal structure of human heparanase in complex with heparin tetrasaccharide DP4
Analyse Crystal structure of human heparanase in complex with heparin tetrasaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E9C
- Type
- protein
- Length
- 459 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparanase
- EC
- 3.2.1.166
- UniProt
- Q9Y251
- Ligands
- 5KV, IDR, UAP, NAG, SGN, CL, SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparanase (EC 3.2.1.166) | protein | 385 | 33% helix, 27% strand | Q9Y251 |
| B | Heparanase (EC 3.2.1.166) | protein | 74 | 34% helix, 32% strand | Q9Y251 |
Ligands and binding sites
- 5KV · 2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose · ligand · chains A, B
- IDR · alpha-L-idopyranuronic acid · ligand · chains A, B
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A, B
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.57 | 0.77 | 36 | 5KV, IDR, SGN |
| 2 | 171 | 0.51 | 0.78 | 22 | empty |
| 3 | 77 | 0.47 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4275 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 5E9C · Crystal structure of human heparanase in complex with heparin tetrasaccharide dp4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y251 · AlphaFold monomer V2.0 prediction for heparanase (Q9Y251) · 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 Q9Y251
- Elsewhere: RCSB PDB 5E9C · PDBe 5E9C · UniProt Q9Y251
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