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Structure of a periplasmic oligogalacturonide binding protein from Yersinia enterocolitica in complex with saturated digalacturonic acid

Analyse Structure of a periplasmic oligogalacturonide binding protein from Yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2UVH
Type: protein
Length: 404 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: YERSINIA ENTEROCOLITICA
Molecule: ABC type periplasmic sugar-binding protein
Ligands: ADA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · resolution 2.2 · 1 distinct chain · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC type periplasmic sugar-binding protein	protein	404	48% helix, 15% strand	—

Ligands and binding sites

ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	477	0.72	0.81	52	ADA
2	91	0.40	0.77	20	empty
3	105	0.37	0.74	16	empty

Compared structures

2UVH · Structure of a periplasmic oligogalacturonide binding protein from yersinia… · 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 2UVH · PDBe 2UVH

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