MolNFT v1 · #77114 · protein

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

3R52: “Structure analysis of a wound-inducible lectin ipomoelin from sweet potato”. X-ray diffraction, 2 ligands (GYP, CD), 4 pockets (best druggability 0.62). MolNFT v1 #77114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3R52
Type: protein
Length: 609 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipomoelin
UniProt: P93193
Ligands: GYP, CD
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Ipomoelin	protein	152	0% helix, 65% strand	P93193
B	Ipomoelin	protein	153	0% helix, 67% strand	P93193

Ligands and binding sites

GYP · methyl alpha-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
CD · Cadmium ion · metal · 3 copies · chains B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.62	0.88	32	empty
2	83	0.60	0.89	29	empty
3	184	0.52	0.78	41	empty
4	137	0.46	0.78	23	empty

Interfaces

6 interfaces between chains.

C–D · 1602 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1588 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 777 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 757 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 157 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3R52 · 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 3R52 · PDBe 3R52 · UniProt P93193

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