MolNFT v1 · #97284 · protein + DNA

Structure of binary complex of cgas with bound dsdna

4K96 · Cyclic gmp-AMP synthase: “Structure of binary complex of cgas with bound dsdna”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.86). MolNFT v1 #97284 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4K96
Type: protein + DNA
Length: 781 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase; DNA-F; DNA-R
EC: 2.7.7.-
UniProt: Q8C6L5
Ligands: ZN
Pockets: 10 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.-)	protein	355	42% helix, 18% strand	Q8C6L5
B	Cyclic gmp-AMP synthase (EC 2.7.7.-)	protein	358	43% helix, 18% strand	Q8C6L5
E, G	DNA-F	dna	17	—	—
F, H	DNA-R	dna	17	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.86	0.87	95	empty
2	124	0.75	0.95	19	empty
3	796	0.73	0.78	55	empty
4	705	0.72	0.79	64	empty
5	640	0.69	0.77	39	empty

Interfaces

11 interfaces between chains.

A–B · 881 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 753 Å² buried · 79 hydrogen bonds · nucleic-nucleic
G–H · 751 Å² buried · 78 hydrogen bonds · nucleic-nucleic
A–E · 526 Å² buried · 6 hydrogen bonds · protein-nucleic
B–G · 490 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

4K96 · Structure of Binary Complex of cGAS with Bound dsDNA · the same entry in another collection · chain H against H, TM-score 1.00
Q8C6L5 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8C6L5) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q8C6L5
Elsewhere: RCSB PDB 4K96 · PDBe 4K96 · UniProt Q8C6L5

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