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The structure of the pea lectin-D-mannopyranose complex

Analyse The structure of the pea lectin-D-mannopyranose complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BQP
Type: protein
Length: 456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (lectin)
UniProt: P02867
Ligands: MAN, BMA, CA, MN
Pockets: 2 · best druggability 0.44

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein (lectin)	protein	181	3% helix, 44% strand	P02867
B, D	Protein (lectin)	protein	47	9% helix, 64% strand	P02867

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
MN · Manganese (II) ion · metal · 2 copies · chains A, C

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	100	0.44	0.79	17	empty
2	86	0.41	0.79	18	empty

Interfaces

5 interfaces between chains.

A–B · 3917 Å² buried · 95 hydrogen bonds · protein-protein
C–D · 3878 Å² buried · 105 hydrogen bonds · protein-protein
A–C · 971 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 154 Å² buried · 1 hydrogen bond · protein-protein
A–D · 131 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1BQP · The structure of the pea lectin-D-mannopyranose complex · the same entry in another collection · chain C against C, TM-score 1.00
P02867 · AlphaFold monomer V2.0 prediction for lectin (P02867) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P02867
Elsewhere: RCSB PDB 1BQP · PDBe 1BQP · UniProt P02867

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