MolNFT v1 · #144650 · protein
Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203C), inactive (T205A), N594S, with ALPHA,BETA-methylene-ATP (ampcpp)
6C02 · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203C), inactive (T205A), N594S…”. X-ray diffraction, 9 ligands (APC, NAG, FUC), 20 pockets (best…
- PDB
- 6C02
- Type
- protein
- Length
- 1,630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 3
- EC
- 3.1.4.1, 3.6.1.9
- UniProt
- O14638
- Ligands
- APC, NAG, FUC, BMA, ZN, CA, NA, SO4, CL
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 3 (EC 3.1.4.1, 3.6.1.9) | protein | 815 | 30% helix, 18% strand | O14638 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 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
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.66 | 0.77 | 58 | CL |
| 2 | 159 | 0.64 | 0.85 | 26 | empty |
| 3 | 152 | 0.61 | 0.84 | 26 | empty |
| 4 | 295 | 0.57 | 0.77 | 33 | empty |
| 5 | 356 | 0.57 | 0.75 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6C02 · 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 6C02 · PDBe 6C02 · UniProt O14638
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