MolNFT v1 · #38130 · protein

P. angolensis lectin (pal) treated with edta for 39 hours

2GNM: “P. angolensis lectin (pal) treated with edta for 39 hours”. X-ray diffraction, 3 ligands (MAN, CA, MN), 2 pockets (best druggability 0.32). MolNFT v1 #38130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GNM
Type: protein
Length: 479 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: Q8GSD2
Ligands: MAN, CA, MN
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	240	4% helix, 48% strand	Q8GSD2
B	Lectin	protein	239	4% helix, 48% strand	Q8GSD2

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains A
CA · Calcium ion · metal · 2 copies · chains A, B
MN · Manganese (II) 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	53	0.32	0.77	15	empty
2	56	0.32	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 920 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

2GNM · P. angolensis lectin (PAL) treated with EDTA for 39 hours · 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 2GNM · PDBe 2GNM · UniProt Q8GSD2

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