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Crystal structure of the nucleosome core particle

Analyse Crystal structure of the nucleosome core particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X1S
Type: protein + DNA
Length: 1,043 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-B; DNA (146-mer)
UniProt: P68431, P62805, P04908, P33778
Ligands: MN, CL
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	96	67% helix, 4% strand	P68431
B	Histone H4	protein	78	65% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
D	Histone H2B type 1-B	protein	94	73% helix, 4% strand	P33778
E	Histone H3.1	protein	98	67% helix, 4% strand	P68431
F	Histone H4	protein	84	61% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	52% helix, 6% strand	P04908
H	Histone H2B type 1-B	protein	92	74% helix, 3% strand	P33778
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains D, C, G, H, I
CL · Chloride ion · ion · 2 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	497	0.77	0.85	46	empty
2	453	0.75	0.85	47	empty
3	420	0.73	0.83	40	empty
4	787	0.70	0.77	57	empty
5	258	0.69	0.85	27	empty

Interfaces

36 interfaces between chains.

I–J · 6372 Å² buried · 521 hydrogen bonds · nucleic-nucleic
E–F · 2680 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2625 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2579 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2540 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3X1S · Crystal structure of the nucleosome core particle · the same entry in another collection · chain J against J, TM-score 1.00
P33778 · AlphaFold monomer V2.0 prediction for histone H2B type 1-B (P33778) · a predicted model of the same protein · chain H against A, TM-score 0.91

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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P33778
Elsewhere: RCSB PDB 3X1S · PDBe 3X1S · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P33778

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