MolNFT v1 · #125113 · protein
N-acetylneuraminate lyase from methicillin-resistant staphylococcus aureus
5KZE: “N-acetylneuraminate lyase from methicillin-resistant staphylococcus aureus”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.74). MolNFT v1 #125113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KZE
- Type
- protein
- Length
- 2,336 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q2FJU9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 292 | 53% helix, 14% strand | Q2FJU9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.74 | 0.91 | 24 | empty |
| 2 | 190 | 0.73 | 0.90 | 28 | empty |
| 3 | 168 | 0.73 | 0.90 | 25 | empty |
| 4 | 175 | 0.72 | 0.90 | 29 | empty |
| 5 | 849 | 0.69 | 0.75 | 63 | empty |
Interfaces
13 interfaces between chains.
- C–G · 1541 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1525 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1508 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1498 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5KZE · N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus · the same entry in another collection · chain H against H, TM-score 1.00
- Q2FJU9 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q2FJU9) · 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 Q2FJU9
- Elsewhere: RCSB PDB 5KZE · PDBe 5KZE · UniProt Q2FJU9
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