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Structural characterization of H3K56Q nucleosomes and nucleosomal arrays

Analyse Structural characterization of H3K56Q nucleosomes and nucleosomal arrays in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KXB
Type: protein + DNA
Length: 1,020 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; Palindromic 146 bp DNA repeat 8/9…
UniProt: P84233, P62799, Q6AZJ8, P02281
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	92	68% helix, 4% strand	P84233
B	Histone H4	protein	74	62% helix, 9% strand	P62799
C	Histone H2A	protein	105	56% helix, 7% strand	Q6AZJ8
D	Histone H2B 1.1	protein	86	77% helix, 5% strand	P02281
E	Histone H3.2	protein	90	69% helix, 4% strand	P84233
F	Histone H4	protein	86	55% helix, 8% strand	P62799
G	Histone H2A	protein	100	53% helix, 7% strand	Q6AZJ8
H	Histone H2B 1.1	protein	95	73% helix, 4% strand	P02281
I, J	Palindromic 146 bp DNA repeat 8/9 from human X-chromosome alpha satellite DNA	dna	146	—	—

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	959	0.81	0.83	88	empty
2	401	0.73	0.84	43	empty
3	297	0.72	0.86	42	empty
4	741	0.69	0.77	52	empty
5	482	0.67	0.79	42	empty

Interfaces

37 interfaces between chains.

I–J · 6380 Å² buried · 523 hydrogen bonds · nucleic-nucleic
E–F · 2575 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2507 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2499 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2403 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3KXB · Structural characterization of H3K56Q nucleosomes and nucleosomal arrays · the same entry in another collection · chain J against J, TM-score 1.00
P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 3KXB · PDBe 3KXB · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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