MolNFT v1 · #114162 · protein + DNA

The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations

5B40 · Histone H3.2: “The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #114162 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B40
Type: protein + DNA
Length: 1,031 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
UniProt: Q71DI3, P62805, P04908, P06899
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 9 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	94	65% helix, 4% strand	Q71DI3
B	Histone H4	protein	78	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	104	56% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	93	74% helix, 4% strand	P06899
E	Histone H3.2	protein	95	65% helix, 4% strand	Q71DI3
F	Histone H4	protein	80	61% helix, 9% strand	P62805
G	Histone H2A type 1-B/E	protein	104	57% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	91	77% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.79	0.83	71	empty
2	450	0.75	0.84	47	empty
3	421	0.73	0.84	43	empty
4	889	0.72	0.77	52	empty
5	521	0.67	0.78	42	empty

Interfaces

37 interfaces between chains.

I–J · 6514 Å² buried · 724 hydrogen bonds · nucleic-nucleic
C–D · 2648 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 2637 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2605 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2515 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5B40 · The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations · 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 A against A, TM-score 0.99

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 P06899
Elsewhere: RCSB PDB 5B40 · PDBe 5B40 · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt P06899

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