MolNFT v1 · #135577 · protein

Crystal structure of native lectin from platypodium elegans seeds (pela) complexed with MAN1-3MAN-ome.

5U38: “Crystal structure of native lectin from platypodium elegans seeds (pela) complexed with MAN1-3MAN-ome.”. X-ray diffraction, 5 ligands (MMA, MAN, NAG), 1 pocket (best druggability 0.36). MolNFT v1 #135577 on GenesisL1: 3D structure…

PDB: 5U38
Type: protein
Length: 239 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: G1EUI6
Ligands: MMA, MAN, NAG, MN, CA
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	239	3% helix, 46% strand	G1EUI6

Ligands and binding sites

MMA · methyl alpha-D-mannopyranoside · sugar · chains A
MAN · alpha-D-mannopyranose · sugar · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
MN · Manganese (II) ion · metal · chains A
CA · Calcium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.36	0.77	16	empty

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

5U38 · Crystal structure of native lectin from Platypodium elegans seeds (PELa) complexed with… · 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 G1EUI6
Elsewhere: RCSB PDB 5U38 · PDBe 5U38 · UniProt G1EUI6

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