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X-ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C

Analyse X-ray crystal structure of a nucleosome core particle with its DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ONW
Type: protein + DNA
Length: 1,045 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (147-mer); Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: MN, CL
Pockets: 20 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	DNA (147-mer)	dna	147	—	—
J	DNA (147-mer)	dna	147	—	—
A	Histone H3.2	protein	96	65% helix, 4% strand	P84233
B	Histone H4	protein	78	64% helix, 9% strand	P62799
C	Histone H2A	protein	103	57% helix, 7% strand	Q6AZJ8
D	Histone H2B 1.1	protein	96	71% helix, 4% strand	P02281
E	Histone H3.2	protein	95	64% helix, 4% strand	P84233
F	Histone H4	protein	86	58% helix, 8% strand	P62799
G	Histone H2A	protein	105	54% helix, 7% strand	Q6AZJ8
H	Histone H2B 1.1	protein	92	74% helix, 4% strand	P02281

Ligands and binding sites

MN · Manganese (II) ion · metal · 20 copies · chains I, J, C, D, E, F
CL · Chloride ion · ion · 4 copies · chains A, J, C, D, E, I, G, H

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	801	0.80	0.83	77	empty
2	474	0.74	0.83	55	empty
3	493	0.73	0.82	55	empty
4	876	0.71	0.77	60	empty
5	662	0.67	0.76	44	empty

Interfaces

35 interfaces between chains.

I–J · 6429 Å² buried · 530 hydrogen bonds · nucleic-nucleic
E–F · 2641 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2639 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2605 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2491 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

5ONW · X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically… · the same entry in another collection · chain I against I, 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 5ONW · PDBe 5ONW · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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