MolNFT v1 · #19070 · protein

Pterocarpus angolensis lectin pal in complex with the dimannoside MAN(ALPHA1-3)MAN

1Q8P: “Pterocarpus angolensis lectin pal in complex with the dimannoside MAN(ALPHA1-3)MAN”. X-ray diffraction, 4 ligands (MMA, MAN, MN), 2 pockets (best druggability 0.34). MolNFT v1 #19070 on GenesisL1: 3D structure, binding sites and…

PDB: 1Q8P
Type: protein
Length: 480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
Ligands: MMA, MAN, MN, CA
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	240	5% helix, 48% strand	—

Ligands and binding sites

MMA · methyl alpha-D-mannopyranoside · sugar · 2 copies · chains A, B
MAN · alpha-D-mannopyranose · 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	58	0.34	0.77	16	empty
2	55	0.32	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 925 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

1Q8P · Pterocarpus angolensis lectin PAL in complex with the dimannoside Man(alpha1-3)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
Elsewhere: RCSB PDB 1Q8P · PDBe 1Q8P

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