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Pterocarpus angolensis lectin (pal) in complex with the trimannoside [MAN(ALPHA1-3)]MAN(ALPHA1-6)MAN

Analyse Pterocarpus angolensis lectin (pal) in complex with the trimannoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q8V
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
Ligands: MAN, 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	protein	241	4% helix, 48% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 5 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	59	0.33	0.76	16	empty
2	55	0.30	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 908 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

1Q8V · Pterocarpus angolensis lectin (PAL) in complex with the trimannoside… · 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
Elsewhere: RCSB PDB 1Q8V · PDBe 1Q8V

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