MolNFT v1 · #180252 · protein + DNA

Nucleosome from a dimeric PRC2 bound to a nucleosome

7KTQ · Histone H3: “Nucleosome from a dimeric PRC2 bound to a nucleosome”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #180252 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KTQ
Type: protein + DNA
Length: 1,083 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Histone H2A; Histone H2B; 601 DNA (167-mer)
UniProt: A0A310TTQ1, P62799, Q6AZJ8, A0A1L8FQA5
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 8 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	99	65% helix, 4% strand	A0A310TTQ1
B, F	Histone H4	protein	79	58% helix, 9% strand	P62799
C	Histone H2A	protein	105	54% helix, 7% strand	Q6AZJ8
D, H	Histone H2B	protein	95	72% helix, 4% strand	A0A1L8FQA5
E	Histone H3	protein	96	67% helix, 4% strand	A0A310TTQ1
G	Histone H2A	protein	104	56% helix, 7% strand	Q6AZJ8
I	601 DNA (167-mer)	dna	164	—	—
J	601 DNA (167-mer)	dna	167	—	—

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	817	0.81	0.84	74	empty
2	554	0.75	0.83	53	empty
3	390	0.73	0.84	49	empty
4	262	0.67	0.84	30	empty
5	242	0.67	0.85	28	empty

Interfaces

36 interfaces between chains.

I–J · 7211 Å² buried · 510 hydrogen bonds · nucleic-nucleic
G–H · 2643 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2630 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2493 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2481 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7KTQ · Nucleosome from a dimeric PRC2 bound to a nucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain B 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 A0A310TTQ1
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt A0A1L8FQA5
Elsewhere: RCSB PDB 7KTQ · PDBe 7KTQ · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQA5

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