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Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6- S-propynyl-beta-D-glucopyranoside (stg)

Analyse Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VC3
Type: protein
Length: 928 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactose-binding lectin
UniProt: P02872
Ligands: QWJ, MN, CA
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Galactose-binding lectin	protein	232	4% helix, 50% strand	P02872

Ligands and binding sites

QWJ · 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside · ligand · 3 copies · chains A, B, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

5 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	878	0.78	0.81	101	empty
2	130	0.47	0.78	31	empty
3	182	0.47	0.75	29	empty
4	137	0.44	0.76	26	empty
5	158	0.43	0.75	28	empty

Interfaces

6 interfaces between chains.

B–C · 986 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 981 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 711 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 623 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 64 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6VC3 · Peanut lectin complexed with S-beta-D-thiogalactopyranosyl… · the same entry in another collection · chain A against A, TM-score 1.00
P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P02872
Elsewhere: RCSB PDB 6VC3 · PDBe 6VC3 · UniProt P02872

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