Research workbench
Crystal structure of N-acetylneuraminic acid lyase from staphylococcus aureus with the chemical modification thia-lysine at position 165 in complex with pyruvate
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
- 4AMA
- Type
- protein
- Length
- 1,176 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
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 293 | 53% helix, 14% strand | Q2G160 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 294 | 53% helix, 14% strand | Q2G160 |
| C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 298 | 52% helix, 14% strand | Q2G160 |
| D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 54% helix, 14% strand | Q2G160 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.73 | 0.91 | 25 | empty |
| 2 | 205 | 0.72 | 0.88 | 30 | empty |
| 3 | 384 | 0.67 | 0.80 | 40 | empty |
| 4 | 370 | 0.67 | 0.80 | 40 | empty |
| 5 | 334 | 0.65 | 0.80 | 40 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1583 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1550 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1203 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1189 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4AMA · Crystal Structure of N-acetylneuraminic acid lyase from Staphylococcus aureus with the… · the same entry in another collection · chain D against D, 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 4AMA · PDBe 4AMA · UniProt Q2G160
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