MolNFT v1 · #171225 · protein
Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 a resolution determined by serial crystallography (ssx) using crystaldirect
6YXH: “Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 a resolution determined by serial crystallography (ssx)…”. X-ray diffraction, 5 ligands (NA, MG, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #171225 on GenesisL1: 3D…
- PDB
- 6YXH
- Type
- protein
- Length
- 350 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline ceramidase 3
- EC
- 3.5.1.-, 3.5.1.23
- UniProt
- Q9NUN7
- Ligands
- NA, MG, ZN, CA, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline ceramidase 3 (EC 3.5.1.-, 3.5.1.23) | protein | 350 | 74% helix, 0% strand | Q9NUN7 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.80 | 0.90 | 44 | ZN |
| 2 | 64 | 0.53 | 0.87 | 14 | empty |
| 3 | 103 | 0.36 | 0.74 | 17 | SO4, MG |
Compared structures
- 6YXH · Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution determined by Serial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NUN7 · AlphaFold monomer V2.0 prediction for alkaline ceramidase 3 (Q9NUN7) · a predicted model of the same protein · chain A against A, TM-score 0.69
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 Q9NUN7
- Elsewhere: RCSB PDB 6YXH · PDBe 6YXH · UniProt Q9NUN7
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