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Crystal structure of human neutral ceramidase with zn-bound phosphate
Analyse Crystal structure of human neutral ceramidase with zn-bound phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WGK
- Type
- protein
- Length
- 1,342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutral ceramidase
- EC
- 3.5.1.23
- UniProt
- Q9NR71
- Ligands
- NAG, BMA, ZN, CA, PO4, CL
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutral ceramidase (EC 3.5.1.23) | protein | 670 | 24% helix, 31% strand | Q9NR71 |
| B | Neutral ceramidase (EC 3.5.1.23) | protein | 672 | 24% helix, 31% strand | Q9NR71 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- CIT · Citric acid · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.71 | 0.82 | 44 | PO4 |
| 2 | 405 | 0.69 | 0.81 | 46 | PO4 |
| 3 | 559 | 0.67 | 0.77 | 39 | empty |
| 4 | 503 | 0.66 | 0.78 | 74 | empty |
| 5 | 267 | 0.60 | 0.79 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 748 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q9NR71
- Elsewhere: RCSB PDB 4WGK · PDBe 4WGK · UniProt Q9NR71
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