MolNFT v1 · #137123 · protein
Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)
5VEN · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5VEN
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5
- EC
- 3.1.-.-
- UniProt
- Q9EQG7
- Ligands
- NAG, MAN, BMA, FUC, ZN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5 (EC 3.1.-.-) | protein | 382 | 31% helix, 23% strand | Q9EQG7 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5 (EC 3.1.-.-) | protein | 373 | 32% helix, 24% strand | Q9EQG7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.69 | 0.80 | 55 | empty |
| 2 | 299 | 0.59 | 0.78 | 33 | empty |
| 3 | 308 | 0.59 | 0.78 | 35 | ZN |
| 4 | 100 | 0.33 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 533 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan (N-glycosylation).
Compared structures
- 5VEN · Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EQG7 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain B 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 Q9EQG7
- Elsewhere: RCSB PDB 5VEN · PDBe 5VEN · UniProt Q9EQG7
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