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Crystal structure of a stable heparanase mutant
Analyse Crystal structure of a stable heparanase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RG8
- Type
- protein
- Length
- 459 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparanase 50 kda subunit; Heparanase 8 kda subunit
- UniProt
- Q9Y251
- Ligands
- NA
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparanase 50 kda subunit | protein | 385 | 33% helix, 27% strand | Q9Y251 |
| B | Heparanase 8 kda subunit | protein | 74 | 32% helix, 32% strand | Q9Y251 |
Ligands and binding sites
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 | 286 | 0.53 | 0.75 | 46 | ACT, NA |
| 2 | 143 | 0.51 | 0.79 | 35 | empty |
| 3 | 96 | 0.44 | 0.79 | 21 | empty |
| 4 | 50 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4284 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (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 7RG8 · PDBe 7RG8 · UniProt Q9Y251
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