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The mouse cgas catalytic domain binding to human nucleosome that purified from HEK293T cells

Analyse The mouse cgas catalytic domain binding to human nucleosome that purified from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X5A
Type: protein + DNA
Length: 1,413 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 0.82

Structure

electron microscopy · 10 distinct chains · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	98	62% helix, 4% strand	Q71DI3
B	Histone H4	protein	80	56% helix, 8% strand	P62805
C	Histone H2A type 1	protein	108	52% helix, 6% strand	P0C0S8
D	Histone H2B type 1-C/E/F/G/I	protein	95	73% helix, 4% strand	P62807
F	Histone H4	protein	81	60% helix, 9% strand	P62805
G	Histone H2A type 1	protein	107	52% helix, 6% strand	P0C0S8
H	Histone H2B type 1-C/E/F/G/I	protein	94	70% helix, 4% strand	P62807
I	DNA (natural)	dna	145	—	—
J	DNA (natural)	dna	145	—	—
K	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	362	42% helix, 18% 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	894	0.82	0.84	96	empty
2	1000	0.82	0.82	113	empty
3	1178	0.79	0.80	111	empty
4	257	0.71	0.87	34	empty
5	241	0.70	0.86	32	empty

Interfaces

37 interfaces between chains.

I–J · 6560 Å² buried · 621 hydrogen bonds · nucleic-nucleic
C–D · 2606 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 2558 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 2511 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 2494 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6X5A · The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T… · the same entry in another collection · chain K against K, TM-score 1.00
Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 6X5A · PDBe 6X5A · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q8C6L5

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