Research workbench

Crystal structure of the native histone octamer to 2.1 ångström resolution, crystalised in the presence of S-nitrosoglutathione

Analyse Crystal structure of the native histone octamer to 2.1 ångström resolution… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ARO
Type: protein
Length: 755 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H2A-IV; Histone H2B; Histone H3; Histone H4-VI
UniProt: P02263, P02279, P84229, P62801
Ligands: CL, PO4
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H2A-IV	protein	106	56% helix, 7% strand	P02263
B	Histone H2B	protein	92	76% helix, 4% strand	P02279
C	Histone H3	protein	95	72% helix, 4% strand	P84229
D	Histone H4-VI	protein	83	60% helix, 8% strand	P62801
E	Histone H2A-IV	protein	104	58% helix, 7% strand	P02263
F	Histone H2B	protein	93	74% helix, 4% strand	P02279
G	Histone H3	protein	98	69% helix, 4% strand	P84229
H	Histone H4-VI	protein	84	60% helix, 8% strand	P62801

Ligands and binding sites

CL · Chloride ion · ion · 23 copies · chains A, G, H, B, C, D, E, F
PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E, F

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.84	0.85	102	CL
2	426	0.76	0.86	48	empty
3	376	0.75	0.86	45	empty
4	74	0.47	0.83	20	empty
5	59	0.37	0.79	12	empty

Interfaces

19 interfaces between chains.

E–F · 2638 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2631 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2624 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2584 Å² buried · 25 hydrogen bonds · protein-protein
A–G · 743 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2ARO · Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised… · the same entry in another collection · chain H against H, TM-score 1.00
P84229 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84229) · a predicted model of the same protein · chain C against A, TM-score 0.98
P02263 · AlphaFold monomer V2.0 prediction for histone H2A-IV (P02263) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P02263
Every structure of UniProt P02279
Every structure of UniProt P84229
Every structure of UniProt P62801
Elsewhere: RCSB PDB 2ARO · PDBe 2ARO · UniProt P02263 · UniProt P02279 · UniProt P84229 · UniProt P62801

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