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Structure of rhamnose bound beta-trefoil lectin from entamoeba histolytica

Analyse Structure of rhamnose bound beta-trefoil lectin from entamoeba histolytica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IFB
Type: protein
Length: 261 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
Ligands: RM4
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	126	10% helix, 43% strand	—
B	Lectin	protein	135	9% helix, 39% strand	—

Ligands and binding sites

RM4 · beta-L-rhamnopyranose · ligand · 2 copies · chains A, B
IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.62	0.87	17	empty

Interfaces

1 interface between chains.

A–B · 791 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6IFB · Structure of rhamnose bound beta-trefoil lectin from Entamoeba histolytica · 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
Elsewhere: RCSB PDB 6IFB · PDBe 6IFB

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