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Virulence-associated protein vapg from the intracellular pathogen rhodococcus equi

Analyse Virulence-associated protein vapg from the intracellular pathogen rhodococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AEO
Type: protein
Length: 220 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: R. equi vapg protein
UniProt: Q9EU62
Ligands: K
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	R. equi vapg protein	protein	110	6% helix, 60% strand	Q9EU62
B	R. equi vapg protein	protein	110	6% helix, 65% strand	Q9EU62

Ligands and binding sites

K · Potassium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.37	0.76	17	empty
2	66	0.34	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 432 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5AEO · Virulence-associated protein VapG from the intracellular pathogen Rhodococcus equi · 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
Every structure of UniProt Q9EU62
Elsewhere: RCSB PDB 5AEO · PDBe 5AEO · UniProt Q9EU62

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