MolNFT v1 · #77113 · protein

Structure analysis of a wound-inducible lectin ipomoelin from sweet potato

3R51: “Structure analysis of a wound-inducible lectin ipomoelin from sweet potato”. X-ray diffraction, 1 ligand (MMA), 1 pocket (best druggability 0.39). MolNFT v1 #77113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3R51
Type: protein
Length: 304 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipomoelin
UniProt: P93193
Ligands: MMA
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ipomoelin	protein	151	2% helix, 66% strand	P93193
B	Ipomoelin	protein	153	0% helix, 66% strand	P93193

Ligands and binding sites

MMA · methyl alpha-D-mannopyranoside · sugar · 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	88	0.39	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 844 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3R51 · Structure analysis of a wound-inducible lectin ipomoelin from sweet potato · the same entry in another collection · chain A against A, TM-score 1.00
P93193 · AlphaFold monomer V2.0 prediction for ipomoelin (P93193) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P93193
Elsewhere: RCSB PDB 3R51 · PDBe 3R51 · UniProt P93193

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