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Crystal structure of a protease-resistant mutant form of human galectin-9

Analyse Crystal structure of a protease-resistant mutant form of human galectin-9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WV6
Type: protein
Length: 568 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-9
UniProt: O00182
Ligands: GAL, BGC, GLC, ZN
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Galectin-9	protein	284	2% helix, 54% strand	O00182

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 10 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.83	0.84	114	EDO
2	114	0.39	0.75	20	empty
3	95	0.36	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 998 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3WV6 · Crystal Structure of a protease-resistant mutant form of human galectin-9 · the same entry in another collection · chain A against A, TM-score 1.00
O00182 · AlphaFold monomer V2.0 prediction for galectin-9 (O00182) · 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 O00182
Elsewhere: RCSB PDB 3WV6 · PDBe 3WV6 · UniProt O00182

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