Research workbench
Precursor of the W11F mutant glycosylasparaginase from flavobacterium meningosepticum
Analyse Precursor of the W11F mutant glycosylasparaginase from flavobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9GAF
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glycosylasparaginase)
- EC
- 3.5.1.26
- UniProt
- Q47898
- Ligands
- GLY
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (glycosylasparaginase) (EC 3.5.1.26) | protein | 290 | 34% helix, 24% strand | Q47898 |
| C | Protein (glycosylasparaginase) (EC 3.5.1.26) | protein | 292 | 33% helix, 24% strand | Q47898 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.62 | 0.85 | 33 | GLY |
| 2 | 153 | 0.60 | 0.84 | 34 | GLY |
| 3 | 62 | 0.56 | 0.89 | 24 | empty |
| 4 | 172 | 0.52 | 0.78 | 21 | empty |
| 5 | 179 | 0.49 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–C · 2144 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 9GAF · Precursor of the W11F mutant glycosylasparaginase from flavobacterium meningosepticum · the same entry in another collection · chain A against A, TM-score 1.00
- Q47898 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q47898
- Elsewhere: RCSB PDB 9GAF · PDBe 9GAF · UniProt Q47898
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