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Sfsting with C-di-gmp single fiber

Analyse Sfsting with C-di-gmp single fiber in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UN8
Type: protein
Length: 1,780 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD-ntase-associated protein 12
EC: 3.2.2.5
UniProt: A0A2T5Y4G4
Ligands: C2E
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 3 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F	CD-ntase-associated protein 12 (EC 3.2.2.5)	protein	297	38% helix, 22% strand	A0A2T5Y4G4
C	CD-ntase-associated protein 12 (EC 3.2.2.5)	protein	296	39% helix, 21% strand	A0A2T5Y4G4
E	CD-ntase-associated protein 12 (EC 3.2.2.5)	protein	296	39% helix, 21% strand	A0A2T5Y4G4

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 · 3 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	977	0.89	0.91	97	empty
2	635	0.86	0.90	57	empty
3	333	0.84	0.94	50	C2E
4	386	0.83	0.92	47	C2E
5	315	0.83	0.93	44	C2E

Interfaces

11 interfaces between chains.

E–F · 2812 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2742 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2673 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1286 Å² buried · 23 hydrogen bonds · protein-protein
B–F · 1278 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

7UN8 · SfSTING with c-di-GMP single fiber · the same entry in another collection · chain F against F, 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 A0A2T5Y4G4
Elsewhere: RCSB PDB 7UN8 · PDBe 7UN8 · UniProt A0A2T5Y4G4

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