MolNFT v1 · #106419 · protein

Crystal structure of a putative transcriptional regulator from listeria monocytogenes egd-E

4RYK · LMO0325 protein: “Crystal structure of a putative transcriptional regulator from listeria monocytogenes egd-E”. X-ray diffraction, 2 ligands (GLC, FRU), 1 pocket (best druggability 0.63). MolNFT v1 #106419 on GenesisL1: 3D…

PDB: 4RYK
Type: protein
Length: 295 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LMO0325 protein
UniProt: Q8YA39
Ligands: GLC, FRU
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LMO0325 protein	protein	295	76% helix, 0% strand	Q8YA39

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains A
FRU · beta-D-fructofuranose · ion · chains A
TLA · L(+)-tartaric acid · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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	451	0.63	0.77	51	PEG

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

4RYK · Crystal structure of a putative transcriptional regulator from Listeria monocytogenes… · 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 Q8YA39
Elsewhere: RCSB PDB 4RYK · PDBe 4RYK · UniProt Q8YA39

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