Research workbench
Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c)
Analyse Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C01
- Type
- protein
- Length
- 1,626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
- EC
- 3.1.4.1, 3.6.1.9
- UniProt
- O14638
- Ligands
- NAG, BMA, FUC, MAN, ZN, CA, NA
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (EC 3.1.4.1, 3.6.1.9) | protein | 819 | 30% helix, 18% strand | O14638 |
| B | Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (EC 3.1.4.1, 3.6.1.9) | protein | 807 | 30% helix, 18% strand | O14638 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 7 copies
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.66 | 0.77 | 58 | empty |
| 2 | 120 | 0.61 | 0.86 | 24 | empty |
| 3 | 136 | 0.60 | 0.84 | 24 | empty |
| 4 | 284 | 0.56 | 0.77 | 34 | empty |
| 5 | 131 | 0.54 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6C01 · Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203C) · the same entry in another collection · chain A against A, TM-score 1.00
- O14638 · 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 O14638
- Elsewhere: RCSB PDB 6C01 · PDBe 6C01 · UniProt O14638
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