MolNFT v1 · #140112 · protein + DNA

Crystal structure of the human nucleosome containing the H2B E76K mutant

5Y0D · Histone H3.1: “Crystal structure of the human nucleosome containing the H2B E76K mutant”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.81). MolNFT v1 #140112 on GenesisL1: 3D structure, binding sites and…

PDB: 5Y0D
Type: protein + DNA
Length: 1,044 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
UniProt: P68431, P62805, P04908, P06899
Ligands: MN, CL
Pockets: 20 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	96	67% helix, 4% strand	P68431
B	Histone H4	protein	77	64% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	108	55% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
E	Histone H3.1	protein	99	65% helix, 4% strand	P68431
F	Histone H4	protein	85	58% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	56% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 10 copies · chains E, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	647	0.81	0.86	71	empty
2	231	0.73	0.88	41	empty
3	781	0.71	0.78	65	empty
4	202	0.71	0.88	35	empty
5	620	0.71	0.79	57	MN

Interfaces

38 interfaces between chains.

I–J · 6450 Å² buried · 605 hydrogen bonds · nucleic-nucleic
E–F · 2625 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2603 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2548 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2548 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5Y0D · Crystal Structure of the human nucleosome containing the H2B E76K mutant · the same entry in another collection · chain A against A, 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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 5Y0D · PDBe 5Y0D · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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