MolNFT v1 · #177227 · protein

Bacterial sting in complex with C-di-gmp

7EBL: “Bacterial sting in complex with C-di-gmp”. X-ray diffraction, 1 ligand (C2E), 3 pockets (best druggability 0.84). MolNFT v1 #177227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EBL
Type: protein
Length: 331 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sting
Ligands: C2E
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sting	protein	164	46% helix, 22% strand	—
B	Sting	protein	167	47% helix, 22% strand	—

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.84	0.91	59	C2E
2	63	0.37	0.79	20	empty
3	59	0.32	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1538 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7EBL · Bacterial STING in complex with c-di-GMP · 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 7EBL · PDBe 7EBL

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