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Crystal structure of human nucleosome core particle containing H3K79Q mutation

Analyse Crystal structure of human nucleosome core particle containing H3K79Q mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AZF
Type: protein + DNA
Length: 1,045 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; 146-mer DNA
UniProt: P68431, P62805, P04908, P06899
Ligands: MN, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	65% helix, 4% strand	P68431
B	Histone H4	protein	78	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	108	56% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	94	73% helix, 4% strand	P06899
E	Histone H3.1	protein	99	66% helix, 4% strand	P68431
F	Histone H4	protein	84	60% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	56% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I	146-mer DNA	dna	145	—	—
J	146-mer DNA	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 12 copies · chains C, D, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, E, G, H, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.80	0.83	70	empty
2	389	0.76	0.86	47	empty
3	489	0.76	0.84	52	empty
4	1054	0.72	0.76	80	empty
5	708	0.71	0.78	76	MN

Interfaces

35 interfaces between chains.

I–J · 6478 Å² buried · 535 hydrogen bonds · nucleic-nucleic
C–D · 2612 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 2609 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2560 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2526 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3AZF · Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation · the same entry in another collection · chain J against J, TM-score 1.00
P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain H 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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 3AZF · PDBe 3AZF · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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