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2.6 ångström crystal structure of the nucleosome core particle assembled with a 146 bp alpha-satellite DNA (NCP146B) derivatized with oxaliplatin

Analyse 2.6 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: 3REK
Type: protein + DNA
Length: 1,049 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A TYPE1; Histone H2B 1.1; DNA (146-mer)
UniProt: P84233, P62799, P06897, P02281
Ligands: PT, MN, SO4
Pockets: 20 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	64% helix, 4% strand	P84233
B	Histone H4	protein	83	60% helix, 8% strand	P62799
C	Histone H2A TYPE1	protein	103	57% helix, 7% strand	P06897
D	Histone H2B 1.1	protein	99	71% helix, 4% strand	P02281
E	Histone H3.2	protein	97	65% helix, 4% strand	P84233
F	Histone H4	protein	78	63% helix, 9% strand	P62799
G	Histone H2A TYPE1	protein	105	56% helix, 7% strand	P06897
H	Histone H2B 1.1	protein	94	73% helix, 4% strand	P02281
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

PT · Platinum (II) ion · metal · 40 copies · chains I, J, B, F, E, A
MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D
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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.81	0.86	81	empty
2	750	0.79	0.83	78	empty
3	351	0.75	0.86	50	empty
4	759	0.69	0.77	56	empty
5	700	0.68	0.76	52	PT

Interfaces

37 interfaces between chains.

I–J · 6469 Å² buried · 585 hydrogen bonds · nucleic-nucleic
A–B · 2683 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2667 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2604 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2578 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3REK · 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp… · the same entry in another collection · chain J against J, 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

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 3REK · PDBe 3REK · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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