MolNFT v1 · #37734 · protein
Wild type glycosylasparaginase from flavobacterium meningosepticum
2GAW: “Wild type glycosylasparaginase from flavobacterium meningosepticum”. X-ray diffraction, 4 pockets (best druggability 0.52). MolNFT v1 #37734 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GAW
- Type
- protein
- Length
- 550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosylasparaginase
- EC
- 3.5.1.26
- UniProt
- Q47898
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycosylasparaginase (EC 3.5.1.26) | protein | 136 | 45% helix, 15% strand | Q47898 |
| B, D | Glycosylasparaginase (EC 3.5.1.26) | protein | 139 | 30% helix, 34% strand | Q47898 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.52 | 0.84 | 24 | empty |
| 2 | 54 | 0.47 | 0.85 | 17 | empty |
| 3 | 146 | 0.45 | 0.77 | 26 | empty |
| 4 | 148 | 0.45 | 0.76 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2661 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2608 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 710 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 708 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2GAW · Wild type glycosylasparaginase from flavobacterium meningosepticum · the same entry in another collection · chain D against D, 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 C 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 2GAW · PDBe 2GAW · UniProt Q47898
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