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Lectin from dioclea grandiflora complexed to trimannoside

Analyse Lectin from dioclea grandiflora complexed to trimannoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DGL
Type: protein
Length: 474 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: P08902
Ligands: MAN, MMA, CA, MN

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	237	4% helix, 46% strand	P08902

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
MMA · methyl alpha-D-mannopyranoside · sugar · 2 copies · chains A, B
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.

Interfaces

1 interface between chains.

A–B · 1115 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1DGL · Lectin from dioclea grandiflora complexed to trimannoside · the same entry in another collection · chain A against A, TM-score 1.00
P08902 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P08902) · 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 P08902
Elsewhere: RCSB PDB 1DGL · PDBe 1DGL · UniProt P08902

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