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Crystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative

Analyse Crystal structure of human galectin-4 C-terminal carbohydrate recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WAB
Type: protein
Length: 551 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-4
UniProt: P56470
Ligands: U61
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Galectin-4	protein	139	2% helix, 50% strand	P56470
B	Galectin-4	protein	133	2% helix, 50% strand	P56470
D	Galectin-4	protein	140	2% helix, 52% strand	P56470

Ligands and binding sites

U61 · 2,6-anhydro-1,4-dideoxy-1-[4-(4-fluorophenyl)-1H-1,2,3-triazol-1-yl]-4-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-L-manno-heptitol · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.53	0.87	22	empty
2	249	0.53	0.76	27	GOL
3	76	0.33	0.75	16	empty
4	66	0.27	0.73	14	empty

Interfaces

5 interfaces between chains.

A–D · 524 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 491 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 328 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 271 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 19 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6WAB · Crystal structure of human galectin-4 C-terminal carbohydrate recognition domain in… · the same entry in another collection · chain A against A, TM-score 1.00
P56470 · AlphaFold monomer V2.0 prediction for galectin-4 (P56470) · a predicted model of the same protein · chain D 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 P56470
Elsewhere: RCSB PDB 6WAB · PDBe 6WAB · UniProt P56470

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