Research workbench
Crystal structure of the wild-type Staphylococcus aureus N- acetylneurminic acid lyase in complex with fluoropyruvate
Analyse Crystal structure of the wild-type Staphylococcus aureus N- acetylneurminic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8G
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.72
- Source
- STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q2G160
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · resolution 1.72 · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 54% helix, 14% strand | Q2G160 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.57 | 0.79 | 25 | empty |
| 2 | 184 | 0.55 | 0.80 | 22 | empty |
| 3 | 79 | 0.35 | 0.76 | 15 | empty |
| 4 | 75 | 0.34 | 0.76 | 15 | empty |
| 5 | 55 | 0.33 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1197 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5A8G · Crystal structure of the wild-type staphylococcus aureus N- acetylneurminic acid lyase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2G160 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q2G160) · a predicted model of the same protein · 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 Q2G160
- Elsewhere: RCSB PDB 5A8G · PDBe 5A8G · UniProt Q2G160
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