Research workbench

Human nucleosome core particle with H2A.X S139E variant

Analyse Human nucleosome core particle with H2A.X S139E variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K1K
Type: protein + DNA
Length: 1,071 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2AX; Histone H2B type 1-J; DNA (145-mer)
UniProt: P68431, P62805, P16104, P06899
Ligands: MN, K, CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 10 distinct chains · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	98	65% helix, 4% strand	P68431
B	Histone H4	protein	87	57% helix, 7% strand	P62805
C	Histone H2AX	protein	111	55% helix, 5% strand	P16104
D	Histone H2B type 1-J	protein	96	73% helix, 4% strand	P06899
E	Histone H3.1	protein	97	65% helix, 4% strand	P68431
F	Histone H4	protein	81	62% helix, 7% strand	P62805
G	Histone H2AX	protein	114	54% helix, 5% strand	P16104
H	Histone H2B type 1-J	protein	97	72% helix, 4% strand	P06899
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 33 copies · chains G, H, I, J
K · Potassium ion · metal · 2 copies · chains 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.79	0.81	79	empty
2	525	0.72	0.81	48	empty
3	450	0.72	0.82	47	empty
4	678	0.68	0.77	50	MN
5	708	0.68	0.76	52	empty

Interfaces

35 interfaces between chains.

I–J · 6609 Å² buried · 631 hydrogen bonds · nucleic-nucleic
A–B · 2658 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2625 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2623 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2601 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6K1K · Human nucleosome core particle with H2A.X S139E variant · the same entry in another collection · chain J against J, TM-score 1.00
P16104 · AlphaFold monomer V2.0 prediction for histone H2AX (P16104) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 P16104
Every structure of UniProt P06899
Elsewhere: RCSB PDB 6K1K · PDBe 6K1K · UniProt P68431 · UniProt P62805 · UniProt P16104 · UniProt P06899

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