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Crystal structure of autotaxin (ENPP2)

Analyse Crystal structure of autotaxin (ENPP2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XR9
Type: protein
Length: 783 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: Q64610
Ligands: NAG, BMA, ZN, CA, IOD, SCN, PO4
Pockets: 12 · 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	783	30% helix, 19% strand	Q64610

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
ZN · Zinc ion · metal · 2 copies · chains A
CA · Calcium ion · metal · chains A
IOD · Iodide ion · ion · 28 copies · chains A
SCN · Thiocyanate ion · ion · 4 copies · chains A
PO4 · Phosphate ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	754	0.75	0.80	68	SCN, PO4, IOD
2	260	0.61	0.80	33	empty
3	227	0.57	0.79	40	IOD
4	200	0.56	0.79	26	empty
5	177	0.54	0.79	31	empty

Modifications

Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

2XR9 · Crystal structure of Autotaxin (ENPP2) · the same entry in another collection · chain A against A, TM-score 1.00
Q64610 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q64610
Elsewhere: RCSB PDB 2XR9 · PDBe 2XR9 · UniProt Q64610

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