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Structure of human cGAS (K394E) bound to the nucleosome

Analyse Structure of human cGAS (K394E) bound to the nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y5D
Type: protein + DNA
Length: 2,830 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.1
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Histone H3.2; Histone H4; Histone H2A type 2-A; Histone H2B type 1-K; DNA (153-mer)…
EC: 2.7.7.86
UniProt: Q71DI3, P62805, Q6FI13, O60814, Q8N884
Ligands: PTD, ZN
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · resolution 4.1 · 16 distinct chains · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, M	Histone H3.2	protein	96	65% helix, 4% strand	Q71DI3
B	Histone H4	protein	81	60% helix, 7% strand	P62805
C	Histone H2A type 2-A	protein	107	53% helix, 7% strand	Q6FI13
D, T	Histone H2B type 1-K	protein	93	74% helix, 4% strand	O60814
F	Histone H4	protein	83	59% helix, 8% strand	P62805
G	Histone H2A type 2-A	protein	108	52% helix, 6% strand	Q6FI13
H	Histone H2B type 1-K	protein	94	70% helix, 4% strand	O60814
I, U	DNA (153-mer)	dna	153	—	—
J, V	DNA (153-mer)	dna	153	—	—
K, L	Cyclic GMP-AMP synthase (EC 2.7.7.86)	protein	362	43% helix, 18% strand	Q8N884
N	Histone H4	protein	79	62% helix, 8% strand	P62805
O	Histone H2A type 2-A	protein	105	53% helix, 6% strand	Q6FI13
P	Histone H2B type 1-K	protein	90	77% helix, 4% strand	O60814
Q	Histone H3.2	protein	94	66% helix, 4% strand	Q71DI3
R	Histone H4	protein	77	64% helix, 8% strand	P62805
S	Histone H2A type 2-A	protein	102	53% helix, 6% strand	Q6FI13

Ligands and binding sites

PTD · Pentanedial · ligand · 9 copies · chains A, B, C, G, K, D, H, M, N, O, S, L, P
ZN · Zinc ion · metal · 2 copies · chains K, L

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	680	0.78	0.83	68	empty
2	674	0.78	0.83	55	empty
3	1066	0.77	0.79	83	empty
4	1078	0.77	0.79	81	empty
5	455	0.75	0.84	48	empty

Interfaces

84 interfaces between chains.

U–V · 6905 Å² buried · 590 hydrogen bonds · nucleic-nucleic
I–J · 6903 Å² buried · 586 hydrogen bonds · nucleic-nucleic
S–T · 2621 Å² buried · 23 hydrogen bonds · protein-protein
O–P · 2613 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2581 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 covalent (covalent ligand).

Compared structures

6Y5D · Structure of human cgas (K394E) bound to the nucleosome · the same entry in another collection · chain K against K, 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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt Q6FI13
Every structure of UniProt O60814
Every structure of UniProt Q8N884
Elsewhere: RCSB PDB 6Y5D · PDBe 6Y5D · UniProt Q71DI3 · UniProt P62805 · UniProt Q6FI13 · UniProt O60814 · UniProt Q8N884

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