MolNFT v1 · #15402 · protein

Pterocarpus angolensis lectin in complex with sucrose

1N3P · Lectin pal: “Pterocarpus angolensis lectin in complex with sucrose”. X-ray diffraction, 4 ligands (GLC, FRU, MN), 2 pockets (best druggability 0.33). MolNFT v1 #15402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1N3P
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin pal
UniProt: Q8GSD2
Ligands: GLC, FRU, MN, CA
Pockets: 2 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin pal	protein	241	4% helix, 48% strand	Q8GSD2

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.33	0.77	16	empty
2	57	0.31	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 928 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1N3P · Pterocarpus angolensis lectin in complex with sucrose · the same entry in another collection · 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 Q8GSD2
Elsewhere: RCSB PDB 1N3P · PDBe 1N3P · UniProt Q8GSD2

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