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2.5 ångström crystal structure of the nucleosome core particle assembled with a 145 bp alpha-satellite DNA (NCP145)

Analyse 2.5 ångström crystal structure of the nucleosome core particle assembled with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3REH
Type: protein + DNA
Length: 1,055 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (145-mer)
UniProt: P84233, P62799, P06897, P02281
Ligands: MN, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	97	66% helix, 4% strand	P84233
B	Histone H4	protein	82	61% helix, 9% strand	P62799
C, G	Histone H2A type 1	protein	106	57% helix, 7% strand	P06897
D, H	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
F	Histone H4	protein	87	59% helix, 8% strand	P62799
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 15 copies · chains E, F, G, H, I, J
SO4 · Sulfate ion · ion · 3 copies · chains C, D, J, 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	927	0.81	0.83	92	empty
2	462	0.74	0.84	49	empty
3	302	0.73	0.86	37	empty
4	712	0.72	0.79	58	SO4
5	706	0.70	0.78	63	empty

Interfaces

37 interfaces between chains.

I–J · 6483 Å² buried · 594 hydrogen bonds · nucleic-nucleic
C–D · 2659 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2625 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2618 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2553 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3REH · 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp… · the same entry in another collection · chain I against I, TM-score 1.00
P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 3REH · PDBe 3REH · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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