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Crystal structure of human nucleosome core particle containing H4K59Q mutation

Analyse Crystal structure of human nucleosome core particle containing H4K59Q mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AZK
Type: protein + DNA
Length: 1,049 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 0.77

Structure

x-ray diffraction · 10 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	66% helix, 4% strand	P68431
B	Histone H4	protein	78	63% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	108	54% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	95	73% helix, 4% strand	P06899
E	Histone H3.1	protein	99	63% helix, 4% strand	P68431
F	Histone H4	protein	84	58% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	105	54% helix, 6% strand	P04908
H	Histone H2B type 1-J	protein	93	73% 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 · 11 copies · chains C, D, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.77	0.84	57	empty
2	564	0.77	0.84	55	empty
3	293	0.73	0.86	36	empty
4	766	0.69	0.76	65	empty
5	277	0.67	0.83	36	empty

Interfaces

35 interfaces between chains.

I–J · 6442 Å² buried · 531 hydrogen bonds · nucleic-nucleic
E–F · 2646 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2590 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2566 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2501 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3AZK · Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q 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 0.98

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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 3AZK · PDBe 3AZK · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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