MolNFT v1 · #147948 · protein + DNA

Nucleosome breathing : class 4

6ESI · Histone H3.2: “Nucleosome breathing : class 4”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #147948 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ESI
Type: protein + DNA
Length: 985 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 (133-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 65% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	66% helix, 1% strand	P84233
B	Histone H4	protein	78	64% helix, 3% strand	P62799
C	Histone H2A	protein	87	62% helix, 1% strand	Q6AZJ8
D	Histone H2B 1.1	protein	92	75% helix, 0% strand	P02281
E	Histone H3.2	protein	87	64% helix, 0% strand	P84233
F	Histone H4	protein	82	62% helix, 1% strand	P62799
G	Histone H2A	protein	102	52% helix, 1% strand	Q6AZJ8
H	Histone H2B 1.1	protein	93	71% helix, 0% strand	P02281
I	DNA (133-mer)	dna	133	—	—
J	DNA (133-mer)	dna	133	—	—

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	301	0.81	0.91	45	empty
2	603	0.79	0.84	82	empty
3	167	0.78	0.94	43	empty
4	315	0.77	0.88	47	empty
5	105	0.77	0.96	21	empty

Interfaces

35 interfaces between chains.

I–J · 7078 Å² buried · 770 hydrogen bonds · nucleic-nucleic
G–H · 2320 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2213 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2087 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 2071 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6ESI · Nucleosome breathing : Class 4 · the same entry in another collection · chain A against A, 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 6ESI · PDBe 6ESI · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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