Research workbench
Crystal structure of autotaxin in complex with compound 10
Analyse Crystal structure of autotaxin in complex with compound 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WAV
- Type
- protein
- Length
- 801 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2
- EC
- 3.1.4.39
- UniProt
- Q9R1E6
- Ligands
- DWV, NAG, MAN, BMA, ZN, CA, NA, K, SCN, SO4
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 801 | 30% helix, 19% strand | Q9R1E6 |
Ligands and binding sites
- DWV · (5Z)-5-(3,4-dichlorobenzylidene)-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4(5H)-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- K · Potassium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 18 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.74 | 0.80 | 51 | DWV |
| 2 | 300 | 0.62 | 0.79 | 30 | EDO |
| 3 | 220 | 0.58 | 0.80 | 32 | empty |
| 4 | 149 | 0.49 | 0.78 | 28 | EDO |
| 5 | 125 | 0.45 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3WAV · Crystal Structure of Autotaxin in Complex with Compound 10 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R1E6 · 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 Q9R1E6
- Elsewhere: RCSB PDB 3WAV · PDBe 3WAV · UniProt Q9R1E6
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