MolNFT v1 · #38120 · protein

Edta-treated (2 weeks) P. angolensis lectin

2GNB: “Edta-treated (2 weeks) P. angolensis lectin”. X-ray diffraction, 1 ligand (MAN), 3 pockets (best druggability 0.40). MolNFT v1 #38120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GNB
Type: protein
Length: 466 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: Q8GSD2
Ligands: MAN
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	237	4% helix, 49% strand	Q8GSD2
B	Lectin	protein	229	5% helix, 50% strand	Q8GSD2

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains B

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

Pockets

3 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	81	0.40	0.78	17	empty
2	60	0.34	0.77	16	empty
3	63	0.33	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 941 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

2GNB · EDTA-treated (2 weeks) P. angolensis lectin · 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 2GNB · PDBe 2GNB · UniProt Q8GSD2

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