MolNFT v1 · #116513 · protein

Sugar binding protein - human galectin-2

5DG1: “Sugar binding protein - human galectin-2”. X-ray diffraction, 2 ligands (BGC, GAL), 7 pockets (best druggability 0.76). MolNFT v1 #116513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DG1
Type: protein
Length: 776 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-2
UniProt: P05162
Ligands: BGC, GAL
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, H, I	Galectin-2	protein	129	0% helix, 58% strand	P05162
B, C	Galectin-2	protein	130	0% helix, 28% strand	P05162

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, D, H, I
GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, D, H, I

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1088	0.76	0.78	109	GAL
2	72	0.74	0.97	19	empty
3	812	0.73	0.78	83	GAL
4	94	0.66	0.90	22	empty
5	74	0.57	0.88	20	empty

Interfaces

8 interfaces between chains.

B–C · 656 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 607 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 584 Å² buried · 13 hydrogen bonds · protein-protein
D–H · 536 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 513 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5DG1 · Sugar binding protein - human galectin-2 · the same entry in another collection · chain I against I, TM-score 1.00
P05162 · AlphaFold monomer V2.0 prediction for galectin-2 (P05162) · 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 P05162
Elsewhere: RCSB PDB 5DG1 · PDBe 5DG1 · UniProt P05162

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