MolNFT v1 · #83016 · protein

Crystal structure of galectin-1 in the lactose-unbound STATE(P212121)

3W59: “Crystal structure of galectin-1 in the lactose-unbound STATE(P212121)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.64). MolNFT v1 #83016 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3W59
Type: protein
Length: 531 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galectin-1
UniProt: P09382
Ligands: SO4
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 1% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Galectin-1	protein	132	0% helix, 64% strand	P09382
B	Galectin-1	protein	132	0% helix, 64% strand	P09382
C	Galectin-1	protein	134	2% helix, 60% strand	P09382
D	Galectin-1	protein	133	0% helix, 56% strand	P09382

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, D, C

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

Pockets

5 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	496	0.64	0.77	49	GOL
2	328	0.62	0.79	41	empty
3	73	0.49	0.84	22	empty
4	50	0.40	0.82	15	empty
5	97	0.34	0.74	20	empty

Interfaces

5 interfaces between chains.

A–B · 606 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 571 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 278 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 157 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 117 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3W59 · Crystal structure of Galectin-1 in the lactose-unbound state(P212121) · 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 0.98

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 3W59 · PDBe 3W59 · UniProt P09382

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.