MolNFT v1 · #57406 · protein + DNA

The nucleosome containing a testis-specific histone variant, human H3T

3A6N · Histone H3.1T: “The nucleosome containing a testis-specific histone variant, human H3T”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.78). MolNFT v1 #57406 on GenesisL1: 3D structure, binding sites and…

PDB: 3A6N
Type: protein + DNA
Length: 1,046 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1T; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; 146-mer DNA
UniProt: Q16695, P62805, P04908, P06899
Ligands: MN, CL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 10 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1T	protein	97	64% helix, 4% strand	Q16695
B	Histone H4	protein	81	60% helix, 7% strand	P62805
C	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	94	72% helix, 4% strand	P06899
E	Histone H3.1T	protein	98	67% helix, 4% strand	Q16695
F	Histone H4	protein	84	60% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	54% helix, 6% strand	P04908
H	Histone H2B type 1-J	protein	93	74% helix, 4% strand	P06899
I	146-mer DNA	dna	145	—	—
J	146-mer DNA	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains C, D, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	548	0.78	0.84	62	empty
2	440	0.77	0.86	56	empty
3	503	0.76	0.84	58	empty
4	660	0.71	0.79	58	empty
5	752	0.71	0.78	59	empty

Interfaces

36 interfaces between chains.

I–J · 6438 Å² buried · 536 hydrogen bonds · nucleic-nucleic
C–D · 2630 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2587 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 2556 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2554 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3A6N · The nucleosome containing a testis-specific histone variant, human H3T · the same entry in another collection · chain J against J, TM-score 1.00
Q16695 · AlphaFold monomer V2.0 prediction for histone H3.1T (Q16695) · a predicted model of the same protein · chain A against A, TM-score 0.99
P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q16695
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 3A6N · PDBe 3A6N · UniProt Q16695 · UniProt P62805 · UniProt P04908 · UniProt P06899

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