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Metal-free (apo-pal) in complex with alpha-D-met-man

Analyse Metal-free (apo-pal) in complex with alpha-D-met-man in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GN3
Type: protein
Length: 459 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: Q8GSD2
Ligands: MAN, MMA, SO4
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	227	3% helix, 50% strand	Q8GSD2
B	Lectin	protein	232	4% helix, 49% strand	Q8GSD2

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains A
MMA · methyl alpha-D-mannopyranoside · sugar · chains B
SO4 · Sulfate ion · ion · 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	55	0.34	0.78	14	empty
2	58	0.33	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 879 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

2GN3 · Metal-free (apo-PAL) in complex with alpha-D-Met-Man · 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 2GN3 · PDBe 2GN3 · UniProt Q8GSD2

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