Research workbench
Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)
Analyse Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B56
- Type
- protein
- Length
- 1,553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 1
- EC
- 3.1.4.1, 3.6.1.9
- UniProt
- P06802
- Ligands
- NAG, MAN, BMA, ZN, CA, PO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 1 (EC 3.1.4.1, 3.6.1.9) | protein | 816 | 29% helix, 19% strand | P06802 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 1 (EC 3.1.4.1, 3.6.1.9) | protein | 737 | 29% helix, 21% strand | P06802 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.70 | 0.76 | 66 | empty |
| 2 | 395 | 0.67 | 0.80 | 51 | PO4 |
| 3 | 440 | 0.66 | 0.78 | 74 | empty |
| 4 | 369 | 0.63 | 0.78 | 46 | PO4 |
| 5 | 288 | 0.62 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4B56 · Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1) · the same entry in another collection · chain A against A, TM-score 1.00
- P06802 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P06802
- Elsewhere: RCSB PDB 4B56 · PDBe 4B56 · UniProt P06802
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