Research workbench

Nucleosome core particle treated with cisplatin

Analyse Nucleosome core particle treated with cisplatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B6F
Type: protein + DNA
Length: 1,083 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; 147-mer DNA
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: MN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 10 distinct chains · 58% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	103	58% helix, 4% strand	P84233
B	Histone H4	protein	79	59% helix, 8% strand	P62799
C	Histone H2A	protein	106	52% helix, 7% strand	Q6AZJ8
D	Histone H2B 1.1	protein	101	68% helix, 4% strand	P02281
E	Histone H3.2	protein	105	58% helix, 3% strand	P84233
F	Histone H4	protein	87	53% helix, 7% strand	P62799
G	Histone H2A	protein	109	47% helix, 6% strand	Q6AZJ8
H	Histone H2B 1.1	protein	99	66% helix, 4% strand	P02281
I	147-mer DNA	dna	147	—	—
J	147-mer DNA	dna	147	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · chains E, F

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	1012	0.83	0.84	85	empty
2	512	0.78	0.85	62	empty
3	582	0.77	0.84	63	empty
4	673	0.73	0.80	59	empty
5	357	0.71	0.84	39	empty

Interfaces

38 interfaces between chains.

I–J · 6470 Å² buried · 586 hydrogen bonds · nucleic-nucleic
C–D · 2687 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2638 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2637 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2490 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3B6F · Nucleosome core particle treated with cisplatin · 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 0.95

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 3B6F · PDBe 3B6F · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.