Research workbench
Crystal structure of N-acetylneuraminic acid lyase from staphylococcus aureus with the chemical modification thia-lysine at position 165
Analyse Crystal structure of N-acetylneuraminic acid lyase from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AHO
- Type
- protein
- Length
- 1,131 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q2G160
- Ligands
- CL
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 283 | 54% helix, 13% strand | Q2G160 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 284 | 54% helix, 13% strand | Q2G160 |
| D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 281 | 54% helix, 14% strand | Q2G160 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.72 | 0.89 | 27 | empty |
| 2 | 185 | 0.71 | 0.89 | 30 | empty |
| 3 | 361 | 0.61 | 0.77 | 39 | CL |
| 4 | 336 | 0.59 | 0.77 | 36 | CL |
| 5 | 317 | 0.58 | 0.76 | 36 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1466 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1418 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1201 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1148 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4AHO · Crystal Structure of N-acetylneuraminic acid lyase from Staphylococcus aureus with the… · 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 D 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 4AHO · PDBe 4AHO · UniProt Q2G160
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