MolNFT v1 · #169234 · protein + DNA

The mouse cgas catalytic domain binding to human assembled nucleosome

6X59 · Histone H3.2: “The mouse cgas catalytic domain binding to human assembled nucleosome”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #169234 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6X59
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; Cyclic…
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, 9% 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	72% helix, 4% strand	P62807
F	Histone H4	protein	81	60% helix, 9% strand	P62805
G	Histone H2A type 1	protein	107	52% helix, 7% strand	P0C0S8
H	Histone H2B type 1-C/E/F/G/I	protein	94	70% helix, 4% strand	P62807
I	DNA	dna	145	—	—
J	DNA	dna	145	—	—
K	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	362	42% 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	974	0.82	0.83	99	empty
2	903	0.77	0.80	93	empty
3	454	0.74	0.84	46	empty
4	258	0.72	0.87	33	empty
5	244	0.72	0.87	31	empty

Interfaces

38 interfaces between chains.

I–J · 6589 Å² buried · 464 hydrogen bonds · nucleic-nucleic
C–D · 2653 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2616 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 2612 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2590 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6X59 · The mouse cGAS catalytic domain binding to human assembled nucleosome · 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 0.98

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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P0C0S8
Every structure of UniProt P62807
Every structure of UniProt Q8C6L5
Elsewhere: RCSB PDB 6X59 · PDBe 6X59 · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q8C6L5

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