Research workbench

Cryo-EM structure of H2BK34UB nucleosome

Analyse Cryo-EM structure of H2BK34UB nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XD0
Type: protein + DNA
Length: 1,207 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H4; Histone H2A; Histone H2B type 1-K; Histone domain-containing protein; DNA…
UniProt: A0A672PXK1, Q08AJ9, Q2M2T1, S4RAZ3, A0A2H6N1E9
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 8 distinct chains · 51% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, B	Histone H4	protein	83	23% helix, 8% strand	A0A672PXK1
G, C	Histone H2A	protein	108	55% helix, 6% strand	Q08AJ9
H, D	Histone H2B type 1-K	protein	92	75% helix, 4% strand	Q2M2T1
E	Histone domain-containing protein	protein	98	61% helix, 2% strand	S4RAZ3
A	Histone domain-containing protein	protein	99	62% helix, 1% strand	S4RAZ3
I	DNA (146-mer)	dna	146	—	—
J	DNA (146-mer)	dna	146	—	—
L, K	Ubiquitin-60S ribosomal protein L40	protein	76	20% helix, 34% strand	A0A2H6N1E9

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	551	0.76	0.83	60	empty
2	406	0.75	0.85	47	empty
3	432	0.75	0.84	53	empty
4	250	0.74	0.89	32	empty
5	221	0.70	0.88	36	empty

Interfaces

41 interfaces between chains.

I–J · 6544 Å² buried · 520 hydrogen bonds · nucleic-nucleic
A–B · 2652 Å² buried · 24 hydrogen bonds · protein-protein
D–C · 2565 Å² buried · 19 hydrogen bonds · protein-protein
F–E · 2559 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 2534 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7XD0 · cryo-EM structure of H2BK34ub nucleosome · the same entry in another collection · chain K against K, 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 A0A672PXK1
Every structure of UniProt Q08AJ9
Every structure of UniProt Q2M2T1
Every structure of UniProt S4RAZ3
Every structure of UniProt A0A2H6N1E9
Elsewhere: RCSB PDB 7XD0 · PDBe 7XD0 · UniProt A0A672PXK1 · UniProt Q08AJ9 · UniProt Q2M2T1 · UniProt S4RAZ3 · UniProt A0A2H6N1E9

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