MolNFT v1 · #134687 · protein
Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine
5TCD · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine”. X-ray diffraction, 7 ligands (PC, NAG, BMA), 1 pocket (best druggability 0.54). MolNFT v1 #134687 on…
- PDB
- 5TCD
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 7
- EC
- 3.1.4.12
- UniProt
- Q6UWV6
- Ligands
- PC, NAG, BMA, FUC, ZN, NA, IOD
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 7 (EC 3.1.4.12) | protein | 388 | 32% helix, 21% strand | Q6UWV6 |
Ligands and binding sites
- PC · Phosphocholine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- IOD · Iodide ion · ion · 37 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.54 | 0.77 | 29 | IOD, PC |
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 5TCD · Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine · the same entry in another collection · chain A against A, TM-score 1.00
- Q6UWV6 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · 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 Q6UWV6
- Elsewhere: RCSB PDB 5TCD · PDBe 5TCD · UniProt Q6UWV6
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