MolNFT v1 · #56985 · protein
Crystal structure analysis of neutral ceramidase from pseudomonas aeruginosa
2ZWS: “Crystal structure analysis of neutral ceramidase from pseudomonas aeruginosa”. X-ray diffraction, 3 ligands (PLM, ZN, MG), 6 pockets (best druggability 0.63). MolNFT v1 #56985 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ZWS
- Type
- protein
- Length
- 630 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutral ceramidase
- EC
- 3.5.1.23
- UniProt
- Q9I596
- Ligands
- PLM, ZN, MG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutral ceramidase (EC 3.5.1.23) | protein | 630 | 23% helix, 32% strand | Q9I596 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 17 copies · chains A
- FMT · Formic acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.63 | 0.80 | 37 | GOL |
| 2 | 71 | 0.49 | 0.84 | 19 | GOL |
| 3 | 178 | 0.42 | 0.73 | 26 | empty |
| 4 | 92 | 0.39 | 0.77 | 18 | GOL |
| 5 | 51 | 0.28 | 0.75 | 18 | GOL |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2ZWS · Crystal Structure Analysis of neutral ceramidase from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I596 · AlphaFold monomer V2.0 prediction for neutral ceramidase (Q9I596) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9I596
- Elsewhere: RCSB PDB 2ZWS · PDBe 2ZWS · UniProt Q9I596
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