MolNFT v1 · #120211 · protein + DNA

Crystal structure of nucleosome complex with human testis-specific histone variants, TH2A

5GT0 · Histone H3.1: “Crystal structure of nucleosome complex with human testis-specific histone variants, TH2A”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #120211 on GenesisL1: 3D structure…

PDB: 5GT0
Type: protein + DNA
Length: 1,059 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-J; DNA (146-mer)
UniProt: P68431, P62805, Q96QV6, P62807
Ligands: MN, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 8 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.1	protein	99	62% helix, 4% strand	P68431
B	Histone H4	protein	79	61% helix, 9% strand	P62805
F	Histone H4	protein	86	58% helix, 8% strand	P62805
C	Histone H2A type 1-a	protein	106	55% helix, 7% strand	Q96QV6
G	Histone H2A type 1-a	protein	106	55% helix, 7% strand	Q96QV6
D	Histone H2B type 1-J	protein	98	71% helix, 4% strand	P62807
H	Histone H2B type 1-J	protein	94	76% helix, 4% strand	P62807
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 14 copies · chains E, F, C, D, J, I, H
CL · Chloride ion · ion · 6 copies · chains E, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1171	0.80	0.81	86	empty
2	467	0.76	0.85	48	empty
3	361	0.70	0.83	45	empty
4	822	0.69	0.76	90	MN
5	721	0.68	0.76	51	empty

Interfaces

37 interfaces between chains.

I–J · 6394 Å² buried · 540 hydrogen bonds · nucleic-nucleic
C–D · 2688 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2661 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2659 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2525 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5GT0 · Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a · the same entry in another collection · chain J against J, TM-score 1.00
Q96QV6 · AlphaFold monomer V2.0 prediction for histone H2A type 1-a (Q96QV6) · a predicted model of the same protein · chain C 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 Q96QV6
Every structure of UniProt P62807
Elsewhere: RCSB PDB 5GT0 · PDBe 5GT0 · UniProt P68431 · UniProt P62805 · UniProt Q96QV6 · UniProt P62807

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