MolNFT v1 · #114066 · protein + DNA

Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122

5B0Y · Histone H3.2: “Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #114066 on GenesisL1: 3D structure…

PDB: 5B0Y
Type: protein + DNA
Length: 1,043 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
Ligands: MN, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	96	66% helix, 4% strand	Q71DI3
B	Histone H4	protein	78	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	93	74% helix, 4% strand	P06899
E	Histone H3.2	protein	99	66% helix, 4% strand	Q71DI3
F	Histone H4	protein	84	60% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	57% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains E, I, J
CL · Chloride ion · ion · 2 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	825	0.80	0.83	74	empty
2	485	0.77	0.85	45	empty
3	490	0.76	0.85	45	empty
4	810	0.70	0.77	56	empty
5	166	0.66	0.87	31	empty

Interfaces

36 interfaces between chains.

I–J · 6461 Å² buried · 631 hydrogen bonds · nucleic-nucleic
E–F · 2669 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2631 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2623 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2554 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5B0Y · Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 · 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 5B0Y · PDBe 5B0Y · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt P06899

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