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Nucleosome core particle with an adduct of a binuclear rapta (ru- arene-phosphaadamantane) compound having an ethylenediamine linker

Analyse Nucleosome core particle with an adduct of a binuclear rapta (ru… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XF6
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; Histone H2B 1.1; DNA (145-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: RUD, EDN, MG, 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	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

RUD · [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 · ligand · 2 copies · chains G, H
EDN · Ethane-1,2-diamine · ligand
MG · Magnesium ion · metal · chains E
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	1122	0.81	0.83	113	empty
2	465	0.74	0.83	49	empty
3	866	0.73	0.78	89	empty
4	293	0.72	0.86	37	empty
5	628	0.71	0.79	51	empty

Interfaces

37 interfaces between chains.

I–J · 6403 Å² buried · 545 hydrogen bonds · nucleic-nucleic
C–D · 2639 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2628 Å² buried · 22 hydrogen bonds · protein-protein
G–H · 2604 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2565 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5XF6 · Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane)… · the same entry in another collection · chain A against A, TM-score 1.00

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 5XF6 · PDBe 5XF6 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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