MolNFT v1 · #147947 · protein + DNA

Nucleosome breathing : class 3

6ESH · Histone H3.2: “Nucleosome breathing : class 3”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #147947 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ESH
Type: protein + DNA
Length: 1,012 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (137-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 10 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	64% helix, 4% strand	P84233
B	Histone H4	protein	81	62% helix, 7% strand	P62799
C	Histone H2A	protein	100	56% helix, 6% strand	Q6AZJ8
D	Histone H2B 1.1	protein	91	75% helix, 4% strand	P02281
E	Histone H3.2	protein	95	66% helix, 4% strand	P84233
F	Histone H4	protein	80	63% helix, 8% strand	P62799
G	Histone H2A	protein	104	53% helix, 6% strand	Q6AZJ8
H	Histone H2B 1.1	protein	89	79% helix, 4% strand	P02281
I	DNA (137-mer)	dna	137	—	—
J	DNA (137-mer)	dna	137	—	—

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	869	0.82	0.84	118	empty
2	525	0.78	0.85	61	empty
3	72	0.74	0.97	21	empty
4	340	0.72	0.85	42	empty
5	552	0.69	0.79	49	empty

Interfaces

36 interfaces between chains.

I–J · 6331 Å² buried · 694 hydrogen bonds · nucleic-nucleic
E–F · 2460 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 2442 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2429 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2380 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6ESH · Nucleosome breathing : Class 3 · the same entry in another collection · chain G against G, 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 Q6AZJ8
Every structure of UniProt P02281
Elsewhere: RCSB PDB 6ESH · PDBe 6ESH · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.