Research workbench

Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex

Analyse Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DNM
Type: protein + DNA
Length: 1,055 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.81
Source: Xenopus laevis; SYNTHETIC CONSTRUCT
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (145-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: RAX, MG, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · resolution 2.81 · 7 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	97	65% helix, 4% strand	P84233
B	Histone H4	protein	82	61% helix, 9% strand	P62799
C, G	Histone H2A	protein	106	57% helix, 7% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	95	73% helix, 4% strand	P02281
F	Histone H4	protein	87	57% helix, 8% strand	P62799
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

RAX · dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium · ligand · 2 copies · chains G, H
MG · Magnesium ion · metal · chains E, F
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	866	0.80	0.83	95	empty
2	290	0.73	0.86	37	empty
3	912	0.72	0.77	59	empty
4	679	0.72	0.79	58	SO4
5	688	0.71	0.79	74	empty

Interfaces

37 interfaces between chains.

I–J · 6394 Å² buried · 587 hydrogen bonds · nucleic-nucleic
C–D · 2630 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2625 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2598 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2552 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5DNM · Nucleosome core particle containing adducts of RUTHENIUM(II)-toluene pta complex · 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
P02281 · AlphaFold monomer V2.0 prediction for histone H2B 1.1 (P02281) · a predicted model of the same protein · chain D against A, TM-score 0.88

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 Q6AZJ8
Every structure of UniProt P02281
Elsewhere: RCSB PDB 5DNM · PDBe 5DNM · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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