Research workbench
Crystal structure of ENPP1 in complex with papg
Analyse Crystal structure of ENPP1 in complex with papg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AEK
- Type
- protein
- Length
- 726 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE 1, isoform CRA_D
- UniProt
- G3X9S2
- Ligands
- A, G, NAG, MAN, ZN, CA, CL
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE 1, isoform CRA_D | protein | 726 | 28% helix, 21% strand | G3X9S2 |
Ligands and binding sites
- A · Adenosine-5'-monophosphate · ligand · chains A
- G · Guanosine-5'-monophosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 6 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.69 | 0.82 | 43 | EDO |
| 2 | 385 | 0.60 | 0.76 | 37 | NAG |
| 3 | 75 | 0.59 | 0.88 | 19 | empty |
| 4 | 277 | 0.58 | 0.78 | 35 | A, G, CL |
| 5 | 126 | 0.55 | 0.82 | 18 | empty |
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6AEK · Crystal structure of ENPP1 in complex with pApG · the same entry in another collection · 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 G3X9S2
- Elsewhere: RCSB PDB 6AEK · PDBe 6AEK · UniProt G3X9S2
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