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The crystal structure of the nucleosome containing H3.3 at 2.18 ångström resolution

Analyse The crystal structure of the nucleosome containing H3.3 at 2.18 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X7X
Type: protein + DNA
Length: 1,044 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
UniProt: P84243, 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 H3.3	protein	96	67% helix, 4% strand	P84243
B	Histone H4	protein	77	64% 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	92	75% helix, 4% strand	P06899
E	Histone H3.3	protein	99	65% helix, 4% strand	P84243
F	Histone H4	protein	86	58% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	90	77% helix, 4% strand	P06899
I	DNA (146-mer)	dna	146	—	—
J	DNA (146-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 13 copies · chains E, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	722	0.80	0.84	67	empty
2	394	0.75	0.86	48	empty
3	323	0.75	0.87	39	empty
4	743	0.71	0.78	64	empty
5	196	0.69	0.88	31	empty

Interfaces

36 interfaces between chains.

I–J · 6446 Å² buried · 624 hydrogen bonds · nucleic-nucleic
E–F · 2643 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2581 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2558 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2537 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5X7X · The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution · the same entry in another collection · chain J against J, TM-score 1.00
P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · 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 P84243
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 5X7X · PDBe 5X7X · UniProt P84243 · UniProt P62805 · UniProt P04908 · UniProt P06899

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