MolNFT v1 · #142762 · protein
Crystal structure of ENPP1 in complex with 3'3'-cgamp
6AEL · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE 1, isoform…: “Crystal structure of ENPP1 in complex with 3'3'-cgamp”. X-ray diffraction, 6 ligands (4BW, NAG, MAN), 12 pockets (best druggability 0.66). MolNFT v1 #142762 on…
- PDB
- 6AEL
- Type
- protein
- Length
- 725 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
- 4BW, NAG, MAN, ZN, CA, CL
- Pockets
- 12 · best druggability 0.66
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 | 725 | 28% helix, 21% strand | G3X9S2 |
Ligands and binding sites
- 4BW · 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9, 2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one · 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 · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.66 | 0.81 | 40 | empty |
| 2 | 323 | 0.64 | 0.80 | 44 | 4BW, CL, EDO |
| 3 | 87 | 0.62 | 0.89 | 19 | empty |
| 4 | 394 | 0.61 | 0.76 | 39 | NAG, EDO |
| 5 | 118 | 0.53 | 0.82 | 18 | empty |
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6AEL · Crystal structure of ENPP1 in complex with 3'3'-cGAMP · 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 6AEL · PDBe 6AEL · UniProt G3X9S2
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