Research workbench
X-ray crystal structure of N-acetylneuraminic acid lyase in complex with pyruvate, with the phenylalanine at position 190 replaced with the non-canonical amino acid dihydroxypropylcysteine.
Analyse X-ray crystal structure of N-acetylneuraminic acid lyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LKY
- Type
- protein
- Length
- 1,163 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 0.75
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 54% helix, 14% strand | Q2G160 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 290 | 54% helix, 14% strand | Q2G160 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 158 | 0.75 | 0.93 | 25 | empty |
| 2 | 180 | 0.73 | 0.90 | 28 | empty |
| 3 | 288 | 0.66 | 0.82 | 35 | empty |
| 4 | 319 | 0.65 | 0.80 | 38 | empty |
| 5 | 341 | 0.65 | 0.80 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1562 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1556 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1222 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1211 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 5LKY · X-ray crystal structure of N-acetylneuraminic acid lyase in complex with pyruvate, with… · 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 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 5LKY · PDBe 5LKY · UniProt Q2G160
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