MolNFT v1 · #117451 · protein
Crystal structure of human heparanase
5E8M: “Crystal structure of human heparanase”. X-ray diffraction, 3 ligands (NAG, FUC, CL), 4 pockets (best druggability 0.53). MolNFT v1 #117451 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E8M
- 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
- NAG, FUC, CL
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparanase (EC 3.2.1.166) | protein | 385 | 32% helix, 27% strand | Q9Y251 |
| B | Heparanase (EC 3.2.1.166) | protein | 74 | 32% helix, 32% strand | Q9Y251 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.53 | 0.75 | 34 | EDO, CL |
| 2 | 139 | 0.51 | 0.79 | 35 | EDO |
| 3 | 130 | 0.48 | 0.78 | 22 | EDO |
| 4 | 51 | 0.28 | 0.75 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 4251 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 disulfide (N-glycosylation, disulfide).
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 Q9Y251
- Elsewhere: RCSB PDB 5E8M · PDBe 5E8M · UniProt Q9Y251
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