Research workbench

Rat galectin-1 complex with lactose

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

PDB: 3M2M
Type: protein
Length: 1,026 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-1
UniProt: P11762
Ligands: BGC, GAL
Pockets: 12 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, H	Galectin-1	protein	132	0% helix, 65% strand	P11762
B, F, G	Galectin-1	protein	122	0% helix, 64% strand	P11762

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, C, D, E, H
GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, C, D, E, H

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

Pockets

12 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	318	0.58	0.77	34	empty
2	87	0.46	0.81	15	empty
3	69	0.43	0.81	15	empty
4	91	0.43	0.79	15	empty
5	89	0.42	0.78	13	empty

Interfaces

10 interfaces between chains.

E–F · 566 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 564 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 556 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 547 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 197 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (oxidation).

Compared structures

3M2M · Rat galectin-1 complex with lactose · the same entry in another collection · chain F against F, TM-score 1.00
P11762 · AlphaFold monomer V2.0 prediction for galectin-1 (P11762) · 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 P11762
Elsewhere: RCSB PDB 3M2M · PDBe 3M2M · UniProt P11762

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