Research workbench

Structure of a human nucleosome at 3.2 a resolution

Analyse Structure of a human nucleosome at 3.2 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T79
Type: protein + DNA
Length: 1,066 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (147-mer)
UniProt: Q71DI3, P62805, P04908, O60814
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 8 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	63% helix, 4% strand	Q71DI3
B	Histone H4	protein	84	58% helix, 8% strand	P62805
C, G	Histone H2A type 1-B/E	protein	110	49% helix, 6% strand	P04908
D, H	Histone H2B type 1-K	protein	95	72% helix, 4% strand	O60814
E	Histone H3.2	protein	97	66% helix, 4% strand	Q71DI3
F	Histone H4	protein	87	56% helix, 8% strand	P62805
I	DNA (147-mer)	dna	145	—	—
J	DNA (147-mer)	dna	145	—	—

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	773	0.79	0.83	79	empty
2	647	0.77	0.83	70	empty
3	341	0.74	0.86	51	empty
4	226	0.72	0.88	34	empty
5	998	0.70	0.75	73	empty

Interfaces

35 interfaces between chains.

I–J · 6530 Å² buried · 487 hydrogen bonds · nucleic-nucleic
A–B · 2715 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2665 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2567 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 2553 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6T79 · Structure of a human nucleosome at 3.2 A resolution · the same entry in another collection · chain J against J, TM-score 1.00
Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt O60814
Elsewhere: RCSB PDB 6T79 · PDBe 6T79 · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814

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