Research workbench
Structure of ENPP6, a choline-specific glycerophosphodiester- phosphodiesterase in complex with phosphocholine
Analyse Structure of ENPP6, a choline-specific glycerophosphodiester- phosphodiesterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EGH
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 6
- EC
- 3.1.4.-, 3.1.4.38
- UniProt
- Q8BGN3
- Ligands
- PC, NAG, FUL, ZN
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 6 (EC 3.1.4.-, 3.1.4.38) | protein | 392 | 34% helix, 22% strand | Q8BGN3 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 6 (EC 3.1.4.-, 3.1.4.38) | protein | 393 | 35% helix, 22% strand | Q8BGN3 |
Ligands and binding sites
- PC · Phosphocholine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.66 | 0.80 | 40 | empty |
| 2 | 351 | 0.65 | 0.80 | 33 | empty |
| 3 | 609 | 0.64 | 0.75 | 46 | empty |
| 4 | 363 | 0.63 | 0.78 | 41 | PC, EDO |
| 5 | 331 | 0.62 | 0.79 | 38 | PC, EDO |
Interfaces
1 interface between chains.
- A–B · 834 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EGH · Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BGN3 · AlphaFold monomer V2.0 prediction for glycerophosphocholine cholinephosphodiesterase… · a predicted model of the same protein · chain B 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 Q8BGN3
- Elsewhere: RCSB PDB 5EGH · PDBe 5EGH · UniProt Q8BGN3
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