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

Analyse Structure analysis of a wound-inducible lectin ipomoelin from sweet potato in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DDN
Type: protein
Length: 616 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipomoelin
UniProt: P93193
Ligands: AMG
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ipomoelin	protein	154	0% helix, 66% strand	P93193

Ligands and binding sites

AMG · methyl alpha-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.51	0.77	37	empty
2	189	0.50	0.77	37	empty
3	51	0.26	0.74	14	empty

Interfaces

6 interfaces between chains.

C–D · 1704 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1665 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 994 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 858 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 292 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4DDN · 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 0.94

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 4DDN · PDBe 4DDN · UniProt P93193

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