MolNFT v1 · #141825 · protein
Crystal structure of N-acetylneuraminate lyase from fusobacterium nucleatum complexed with pyruvate
5ZKA: “Crystal structure of N-acetylneuraminate lyase from fusobacterium nucleatum complexed with pyruvate”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #141825 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZKA
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q8RDN6
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 292 | 54% helix, 14% strand | Q8RDN6 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 294 | 51% helix, 13% strand | Q8RDN6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 390 | 0.70 | 0.82 | 55 | EDO |
| 2 | 245 | 0.55 | 0.77 | 29 | EDO |
| 3 | 61 | 0.44 | 0.83 | 15 | empty |
| 4 | 106 | 0.37 | 0.75 | 20 | empty |
| 5 | 73 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1147 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5ZKA · Crystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8RDN6 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q8RDN6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8RDN6
- Elsewhere: RCSB PDB 5ZKA · PDBe 5ZKA · UniProt Q8RDN6
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