MolNFT v1 · #24800 · protein

Peanut lectin with 9MER peptide (iwssagnva)

1V6M · Galactose-binding lectin: “Peanut lectin with 9MER peptide (iwssagnva)”. X-ray diffraction, 2 ligands (CA, MN), 13 pockets (best druggability 0.76). MolNFT v1 #24800 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V6M
Type: protein
Length: 1,856 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactose-binding lectin
UniProt: P02872
Ligands: CA, MN
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Galactose-binding lectin	protein	232	4% helix, 49% strand	P02872

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	769	0.76	0.81	90	empty
2	1116	0.75	0.78	105	empty
3	61	0.62	0.92	28	empty
4	140	0.48	0.78	33	empty
5	171	0.46	0.76	24	empty

Interfaces

13 interfaces between chains.

F–G · 987 Å² buried · 15 hydrogen bonds · protein-protein
E–H · 973 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 967 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 966 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 681 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1V6M · Peanut Lectin with 9mer peptide (IWSSAGNVA) · the same entry in another collection · chain H against H, 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 1V6M · PDBe 1V6M · UniProt P02872

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