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The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.

Analyse The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PA7
Type: protein + DNA
Length: 2,100 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (167-mer); DNA…
EC: 2.1.1.37
UniProt: P84233, P62799, P06897, P02281, Q9Y6K1, Q9UBC3
Ligands: SAH, CL
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 12 distinct chains · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	99	67% helix, 4% strand	P84233
B	Histone H4	protein	81	60% helix, 9% strand	P62799
C	Histone H2A type 1	protein	108	52% helix, 6% strand	P06897
D	Histone H2B 1.1	protein	94	72% helix, 4% strand	P02281
E	Histone H3.2	protein	98	67% helix, 4% strand	P84233
F	Histone H4	protein	83	60% helix, 8% strand	P62799
G	Histone H2A type 1	protein	111	50% helix, 6% strand	P06897
H	Histone H2B 1.1	protein	96	69% helix, 4% strand	P02281
I	DNA (167-mer)	dna	166	—	—
J	DNA (167-mer)	dna	166	—	—
K, P	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	288	30% helix, 17% strand	Q9Y6K1
N, S	DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37)	protein	211	33% helix, 16% strand	Q9UBC3

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains K, P
CL · Chloride ion · ion · 3 copies · chains A, C, D, I, G, H, J

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	762	0.83	0.86	90	empty
2	420	0.78	0.87	74	empty
3	325	0.77	0.88	51	empty
4	910	0.75	0.78	92	empty
5	755	0.73	0.79	82	empty

Interfaces

46 interfaces between chains.

I–J · 7494 Å² buried · 641 hydrogen bonds · nucleic-nucleic
G–H · 2699 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2609 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2589 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 2476 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6PA7 · The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. · the same entry in another collection · chain N against N, 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 P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Every structure of UniProt Q9Y6K1
Every structure of UniProt Q9UBC3
Elsewhere: RCSB PDB 6PA7 · PDBe 6PA7 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q9Y6K1 · UniProt Q9UBC3

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