Research workbench
Crystal structure of mouse autotaxin in complex with 18:1-lpa
Analyse Crystal structure of mouse autotaxin in complex with 18:1-lpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NKP
- Type
- protein
- Length
- 788 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
- NKP, NAG, MAN, BMA, ZN, CA, NA, K, SCN
- Pockets
- 14 · best druggability 0.75
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 | 788 | 30% helix, 19% strand | Q9R1E6 |
Ligands and binding sites
- NKP · (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate · 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
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.75 | 0.79 | 59 | ZN, NKP |
| 2 | 311 | 0.62 | 0.79 | 31 | EDO |
| 3 | 247 | 0.58 | 0.79 | 31 | empty |
| 4 | 200 | 0.56 | 0.79 | 28 | EDO |
| 5 | 86 | 0.45 | 0.80 | 17 | EDO |
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3NKP · Crystal structure of mouse autotaxin in complex with 18:1-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 3NKP · PDBe 3NKP · UniProt Q9R1E6
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