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VIRB8 domain of prgl from enterococcus faecalis PCF10

Analyse VIRB8 domain of prgl from enterococcus faecalis PCF10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AED
Type: protein
Length: 266 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prgl
UniProt: D1LHF8
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prgl	protein	128	27% helix, 45% strand	D1LHF8
B	Prgl	protein	138	25% helix, 41% strand	D1LHF8

Ligands and binding sites

BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

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	547	0.74	0.82	49	BTB
2	206	0.55	0.79	29	BTB
3	81	0.34	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 1038 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7AED · VirB8 domain of PrgL from Enterococcus faecalis pCF10 · 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 D1LHF8
Elsewhere: RCSB PDB 7AED · PDBe 7AED · UniProt D1LHF8

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