MolNFT v1 · #178868 · protein + DNA

1:1 cgas-nucleosome complex

7JO9 · Histone H3.2: “1:1 cgas-nucleosome complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.79). MolNFT v1 #178868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JO9
Type: protein + DNA
Length: 1,415 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; DNA…
EC: 2.7.7.86
UniProt: Q71DI3, P62805, P0C0S8, P62807, Q8C6L5
Ligands: ZN
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 9 distinct chains · 54% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	61% helix, 4% strand	Q71DI3
B	Histone H4	protein	81	62% helix, 7% strand	P62805
C, G	Histone H2A type 1	protein	109	49% helix, 4% strand	P0C0S8
D, H	Histone H2B type 1-C/E/F/G/I	protein	94	73% helix, 2% strand	P62807
E	Histone H3.2	protein	97	65% helix, 4% strand	Q71DI3
F	Histone H4	protein	85	58% helix, 7% strand	P62805
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—
K	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	358	44% helix, 16% strand	Q8C6L5

Ligands and binding sites

ZN · Zinc ion · metal · chains K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1045	0.79	0.80	95	empty
2	730	0.76	0.81	80	empty
3	541	0.73	0.81	49	empty
4	290	0.72	0.86	32	empty
5	630	0.72	0.80	48	empty

Interfaces

37 interfaces between chains.

I–J · 6571 Å² buried · 491 hydrogen bonds · nucleic-nucleic
E–F · 2698 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 2613 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 2606 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2586 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7JO9 · 1:1 cGAS-nucleosome complex · the same entry in another collection · chain K against K, TM-score 1.00
P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P0C0S8
Every structure of UniProt P62807
Every structure of UniProt Q8C6L5
Elsewhere: RCSB PDB 7JO9 · PDBe 7JO9 · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q8C6L5

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