MolNFT v1 · #72850 · protein
Crystal structure of mouse autotaxin in complex with 14:0-lpa
3NKN · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of mouse autotaxin in complex with 14:0-lpa”. X-ray diffraction, 9 ligands (NKN, NAG, MAN), 12 pockets (best druggability 0.76). MolNFT v1 #72850 on…
- PDB
- 3NKN
- Type
- protein
- Length
- 782 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
- NKN, NAG, MAN, BMA, ZN, CA, NA, K, SCN
- Pockets
- 12 · best druggability 0.76
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 | 782 | 30% helix, 19% strand | Q9R1E6 |
Ligands and binding sites
- NKN · (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate · ligand · 2 copies · 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
- EDO · 1,2-ethanediol · additive · 21 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 | 758 | 0.76 | 0.80 | 49 | NKN |
| 2 | 297 | 0.61 | 0.79 | 31 | EDO |
| 3 | 254 | 0.59 | 0.79 | 32 | empty |
| 4 | 175 | 0.54 | 0.79 | 30 | EDO |
| 5 | 178 | 0.53 | 0.78 | 24 | EDO |
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3NKN · Crystal structure of mouse autotaxin in complex with 14:0-LPA · 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 3NKN · PDBe 3NKN · UniProt Q9R1E6
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