Research workbench

Salmonella typhimurium virg-like (stv) protein at 2.19 ångström resolution solved by iodine sad.

Analyse Salmonella typhimurium virg-like (stv) protein at 2.19 ångström resolution… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IO8
Type: protein
Length: 205 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virg-like protein
Ligands: NA, IOD, PO4
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Virg-like protein	protein	104	74% helix, 0% strand	—
B	Virg-like protein	protein	101	74% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 5 copies · chains A, B
IOD · Iodide ion · ion · 14 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.56	0.77	20	IOD
2	126	0.49	0.79	15	IOD

Interfaces

1 interface between chains.

A–B · 1290 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5IO8 · Salmonella Typhimurium VirG-like (STV) protein at 2.19 Angstrom resolution solved by… · 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 5IO8 · PDBe 5IO8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.