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Structure of autotaxin (ENPP2) with LM350

Analyse Structure of autotaxin (ENPP2) with LM350 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LQQ
Type: protein
Length: 775 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: 72P, MAN, NAG, BMA, ZN, CA, NA, IOD
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39)	protein	775	29% helix, 19% strand	Q64610

Ligands and binding sites

72P · 3-(6-chloranyl-2-methyl-1-phenyl-indol-3-yl) sulfanylbenzoic acid · ligand · chains A
MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
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
NA · Sodium ion · metal · chains A
IOD · Iodide ion · ion · 10 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	959	0.77	0.79	85	ZN, IOD, 72P
2	329	0.61	0.78	28	empty
3	275	0.57	0.77	28	empty
4	121	0.57	0.84	20	empty
5	154	0.48	0.77	26	IOD

Modifications

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

Compared structures

5LQQ · Structure of Autotaxin (ENPP2) with LM350 · 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 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 Q64610
Elsewhere: RCSB PDB 5LQQ · PDBe 5LQQ · UniProt Q64610

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