MolNFT v1 · #15419 · protein

Isolectin B4 from vicia villosa in complex with the tn antigen

1N47: “Isolectin B4 from vicia villosa in complex with the tn antigen”. X-ray diffraction, 6 ligands (SER, NAG, FUC), 2 pockets (best druggability 0.68). MolNFT v1 #15419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1N47
Type: protein
Length: 932 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isolectin B4
UniProt: P56625
Ligands: SER, NAG, FUC, A2G, CA, MN
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Isolectin B4	protein	233	4% helix, 45% strand	P56625

Ligands and binding sites

SER · Serine · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) 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

2 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	682	0.68	0.77	80	empty
2	706	0.68	0.77	82	empty

Interfaces

4 interfaces between chains.

C–D · 996 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 996 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 767 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 766 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (N-glycosylation).

Compared structures

1N47 · Isolectin B4 from Vicia villosa in complex with the Tn antigen · the same entry in another collection · chain A against A, TM-score 1.00
P56625 · AlphaFold monomer V2.0 prediction for lectin B4 (P56625) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 P56625
Elsewhere: RCSB PDB 1N47 · PDBe 1N47 · UniProt P56625

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