MolNFT v1 · #147411 · protein

Glutamylation domain, tbtb, from thiomuracin biosynthesis bound to 5'- phosphodesmethylglutamycin

6EC8 · Lantibiotic dehydratase domain protein: “Glutamylation domain, tbtb, from thiomuracin biosynthesis bound to 5'- phosphodesmethylglutamycin”. X-ray diffraction, 1 ligand (J4G), 11 pockets (best druggability 0.81). MolNFT v1 #147411…

PDB: 6EC8
Type: protein
Length: 803 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lantibiotic dehydratase domain protein
UniProt: D6Y502
Ligands: J4G
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lantibiotic dehydratase domain protein	protein	803	44% helix, 18% strand	D6Y502

Ligands and binding sites

J4G · 3'-deoxy-3'-[(L-alpha-glutamyl)amino]adenosine 5'-(dihydrogen phosphate) · ligand · chains A

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.81	0.82	131	J4G
2	122	0.61	0.86	31	empty
3	275	0.61	0.79	31	empty
4	127	0.53	0.81	22	empty
5	50	0.47	0.86	19	empty

Compared structures

6EC8 · Glutamylation domain, TbtB, from thiomuracin biosynthesis bound to… · 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 D6Y502
Elsewhere: RCSB PDB 6EC8 · PDBe 6EC8 · UniProt D6Y502

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