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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: 3R50
Type: protein
Length: 764 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipomoelin
UniProt: P93193
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Ipomoelin	protein	153	0% helix, 67% strand	P93193
B	Ipomoelin	protein	154	0% helix, 64% strand	P93193
E	Ipomoelin	protein	151	0% helix, 64% strand	P93193

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	397	0.61	0.76	36	empty
2	172	0.50	0.78	36	empty
3	172	0.48	0.77	34	empty

Interfaces

7 interfaces between chains.

A–B · 1701 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1641 Å² buried · 41 hydrogen bonds · protein-protein
B–D · 954 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 834 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 617 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3R50 · Structure analysis of a wound-inducible lectin ipomoelin from sweet potato · the same entry in another collection · chain E against E, TM-score 1.00
P93193 · AlphaFold monomer V2.0 prediction for ipomoelin (P93193) · a predicted model of the same protein · chain E 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 3R50 · PDBe 3R50 · UniProt P93193

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