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Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, TH2A and TH2B

Analyse Crystal structure of nucleosome core particle consisting of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GSU
Type: protein + DNA
Length: 1,057 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-a; Histone H2B type 1-a; DNA (146-mer)
UniProt: P68431, P62805, Q96QV6, Q96A08
Ligands: MN, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.1	protein	99	64% helix, 4% strand	P68431
B	Histone H4	protein	79	61% helix, 9% strand	P62805
F	Histone H4	protein	86	57% helix, 8% strand	P62805
C	Histone H2A type 1-a	protein	106	56% helix, 7% strand	Q96QV6
G	Histone H2A type 1-a	protein	105	55% helix, 7% strand	Q96QV6
D	Histone H2B type 1-a	protein	97	71% helix, 4% strand	Q96A08
H	Histone H2B type 1-a	protein	94	76% helix, 4% strand	Q96A08
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 15 copies · chains C, D, I, J
CL · Chloride ion · ion · 3 copies · chains G, H, I, J

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	751	0.81	0.84	67	empty
2	551	0.73	0.81	50	empty
3	483	0.72	0.82	45	empty
4	767	0.70	0.77	55	empty
5	315	0.65	0.81	40	empty

Interfaces

36 interfaces between chains.

I–J · 6398 Å² buried · 527 hydrogen bonds · nucleic-nucleic
E–F · 2655 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2642 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2622 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2486 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

5GSU · Crystal structure of nucleosome core particle consisting of human testis-specific histone… · the same entry in another collection · chain J against J, TM-score 1.00
Q96A08 · AlphaFold monomer V2.0 prediction for histone H2B type 1-a (Q96A08) · a predicted model of the same protein · chain H against A, TM-score 0.96
Q96QV6 · AlphaFold monomer V2.0 prediction for histone H2A type 1-a (Q96QV6) · 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
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Every structure of UniProt Q96QV6
Every structure of UniProt Q96A08
Elsewhere: RCSB PDB 5GSU · PDBe 5GSU · UniProt P68431 · UniProt P62805 · UniProt Q96QV6 · UniProt Q96A08

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