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Crystal structure of human galectin-9 ncrd with selenolactose

Analyse Crystal structure of human galectin-9 ncrd with selenolactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WLU
Type: protein
Length: 568 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-9
UniProt: O00182
Ligands: LSE
Pockets: 3 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Galectin-9	protein	142	2% helix, 54% strand	O00182

Ligands and binding sites

LSE · 2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D

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	942	0.68	0.74	112	LSE
2	127	0.41	0.75	23	empty
3	63	0.37	0.79	18	empty

Interfaces

4 interfaces between chains.

B–C · 448 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 417 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 304 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 256 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3WLU · Crystal Structure of human galectin-9 NCRD with Selenolactose · 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 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 O00182
Elsewhere: RCSB PDB 3WLU · PDBe 3WLU · UniProt O00182

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