MolNFT v1 · #141804 · protein
Crystal structure of N-acetylneuraminate lyase from fusobacterium nucleatum
5ZJM: “Crystal structure of N-acetylneuraminate lyase from fusobacterium nucleatum”. X-ray diffraction, 6 pockets (best druggability 0.52). MolNFT v1 #141804 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZJM
- Type
- protein
- Length
- 1,162 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
- Q8RDN6
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 290 | 52% helix, 13% strand | Q8RDN6 |
| B, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 51% helix, 13% strand | Q8RDN6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.52 | 0.77 | 32 | empty |
| 2 | 199 | 0.51 | 0.77 | 29 | empty |
| 3 | 207 | 0.51 | 0.76 | 29 | empty |
| 4 | 202 | 0.50 | 0.76 | 29 | empty |
| 5 | 66 | 0.44 | 0.82 | 13 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1179 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1160 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5ZJM · Crystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum · the same entry in another collection · chain D against D, 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 0.96
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 5ZJM · PDBe 5ZJM · UniProt Q8RDN6
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