Research workbench
Hyaluronidase in complex with a monoclonal IgG Fab fragment
Analyse Hyaluronidase in complex with a monoclonal IgG Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J88
- Type
- protein
- Length
- 655 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- APIS MELLIFERA; MUS MUSCULUS
- Molecule
- Hyalurononglucosaminidase; Fab
- EC
- 3.2.1.35
- UniProt
- Q08169
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyalurononglucosaminidase (EC 3.2.1.35) | protein | 319 | 48% helix, 15% strand | Q08169 |
| H | Fab | protein | 162 | 4% helix, 50% strand | — |
| L | Fab | protein | 174 | 2% helix, 49% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.51 | 0.77 | 31 | empty |
| 2 | 121 | 0.36 | 0.73 | 23 | empty |
| 3 | 84 | 0.36 | 0.75 | 16 | empty |
| 4 | 97 | 0.34 | 0.74 | 16 | empty |
| 5 | 90 | 0.33 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1167 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 468 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 428 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 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 Q08169
- Elsewhere: RCSB PDB 2J88 · PDBe 2J88 · UniProt Q08169
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