Research workbench
Structure of ENPP6, a choline-specific glycerophosphodiester- phosphodiesterase
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
- 5EGE
- Type
- protein
- Length
- 1,568 residues
- Chains
- 4
- 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
- NAG, FUL, ZN
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 6 (EC 3.1.4.-, 3.1.4.38) | protein | 392 | 35% helix, 22% strand | Q8BGN3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.72 | 0.76 | 71 | EDO |
| 2 | 306 | 0.68 | 0.83 | 33 | empty |
| 3 | 344 | 0.67 | 0.82 | 34 | empty |
| 4 | 410 | 0.66 | 0.79 | 44 | empty |
| 5 | 390 | 0.64 | 0.78 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 839 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 833 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 399 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 4 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5EGE · Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase · the same entry in another collection · chain D against D, TM-score 1.00
- Q8BGN3 · AlphaFold monomer V2.0 prediction for glycerophosphocholine cholinephosphodiesterase… · a predicted model of the same protein · chain C 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 5EGE · PDBe 5EGE · UniProt Q8BGN3
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