MolNFT v1 · #137122 · protein
Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)
5VEM · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)”. X-ray diffraction, 3 ligands (NAG, FUC, ZN), 7 pockets (best druggability 0.60). MolNFT v1 #137122…
- PDB
- 5VEM
- Type
- protein
- Length
- 1,140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5
- EC
- 3.1.-.-
- UniProt
- Q9UJA9
- Ligands
- NAG, FUC, ZN
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5 (EC 3.1.-.-) | protein | 383 | 31% helix, 22% strand | Q9UJA9 |
| C | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 5 (EC 3.1.-.-) | protein | 374 | 32% helix, 23% strand | Q9UJA9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · chains B
- ZN · Zinc ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.60 | 0.77 | 34 | ZN |
| 2 | 350 | 0.58 | 0.76 | 31 | empty |
| 3 | 351 | 0.57 | 0.76 | 30 | empty |
| 4 | 75 | 0.30 | 0.73 | 15 | empty |
| 5 | 56 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 227 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan (N-glycosylation).
Compared structures
- 5VEM · Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJA9 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain C 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 Q9UJA9
- Elsewhere: RCSB PDB 5VEM · PDBe 5VEM · UniProt Q9UJA9
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