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Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment

Analyse Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AOI
Type: protein + DNA
Length: 1,097 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palindromic 146 bp DNA repeat 8/9 from human X- chromosome alpha satellite DNA; Histone…
UniProt: P02302, P62799, P06897, P02281
Ligands: MN
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 59% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146 bp DNA repeat 8/9 from human X- chromosome alpha satellite DNA	dna	146	—	—
A	Histone H3	protein	98	67% helix, 4% strand	P02302
B	Histone H4	protein	83	60% helix, 7% strand	P62799
C	Histone H2A	protein	115	55% helix, 5% strand	P06897
D, H	Histone H2B	protein	99	70% helix, 4% strand	P02281
E	Histone H3	protein	116	55% helix, 3% strand	P02302
F	Histone H4	protein	87	57% helix, 7% strand	P62799
G	Histone H2A	protein	108	54% helix, 6% strand	P06897

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains I, J

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	519	0.76	0.84	50	empty
2	531	0.75	0.83	59	empty
3	546	0.75	0.82	58	empty
4	704	0.68	0.76	57	MN
5	765	0.67	0.75	41	empty

Interfaces

37 interfaces between chains.

I–J · 6381 Å² buried · 569 hydrogen bonds · nucleic-nucleic
E–F · 2641 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2636 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2626 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2624 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1AOI · Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment · the same entry in another collection · chain H against H, TM-score 1.00
P02302 · AlphaFold monomer V2.0 prediction for histone H3.3C (P02302) · a predicted model of the same protein · chain A against A, TM-score 0.98
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain G 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 P02302
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 1AOI · PDBe 1AOI · UniProt P02302 · UniProt P62799 · UniProt P06897 · UniProt P02281

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