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Crystal structure of galectin-1 in complex with N-acetyllactosamine

Analyse Crystal structure of galectin-1 in complex with N-acetyllactosamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q26
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-1
UniProt: P09382
Ligands: NDG, GAL
Pockets: 5 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G, H	Galectin-1	protein	133	0% helix, 60% strand	P09382

Ligands and binding sites

NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, G, H
GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, G, H
GOL · Glycerol · additive · chains G, H

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.48	0.82	17	empty
2	91	0.43	0.79	18	empty
3	76	0.41	0.79	18	GOL
4	88	0.41	0.78	17	empty
5	102	0.34	0.73	23	empty

Interfaces

3 interfaces between chains.

A–B · 615 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 599 Å² buried · 14 hydrogen bonds · protein-protein
A–G · 255 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

4Q26 · Crystal Structure of Galectin-1 in Complex with N-Acetyllactosamine · the same entry in another collection · chain A against A, TM-score 1.00
P09382 · AlphaFold monomer V2.0 prediction for galectin-1 (P09382) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P09382
Elsewhere: RCSB PDB 4Q26 · PDBe 4Q26 · UniProt P09382

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