MolNFT v1 · #62162 · protein
Heparinaseii H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate
3E7J · Heparinase II protein: “Heparinaseii H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate”. X-ray diffraction, 4 ligands (GCD, NAG, GCU), 13 pockets (best druggability 0.76). MolNFT v1 #62162 on…
- PDB
- 3E7J
- Type
- protein
- Length
- 1,486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparinase II protein
- UniProt
- Q46080
- Ligands
- GCD, NAG, GCU, ZN
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heparinase II protein | protein | 743 | 30% helix, 26% strand | Q46080 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GCU · alpha-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.76 | 0.80 | 93 | empty |
| 2 | 754 | 0.69 | 0.76 | 74 | NAG, GCU, GCD |
| 3 | 637 | 0.66 | 0.76 | 57 | NAG, GCU, GCD |
| 4 | 177 | 0.52 | 0.78 | 20 | ACT |
| 5 | 181 | 0.52 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1417 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3E7J · HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide… · 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 3E7J · PDBe 3E7J · UniProt Q46080
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