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The nucleosome containing human TSH2B

Analyse The nucleosome containing human TSH2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WKJ
Type: protein + DNA
Length: 1,043 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-a; DNA (145-mer)
UniProt: P68431, P62805, P04908, Q96A08
Ligands: MN, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 10 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	64% helix, 4% strand	P68431
B	Histone H4	protein	78	64% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	107	55% helix, 6% strand	P04908
D	Histone H2B type 1-a	protein	93	72% helix, 4% strand	Q96A08
E	Histone H3.1	protein	98	65% helix, 4% strand	P68431
F	Histone H4	protein	84	60% helix, 7% strand	P62805
G	Histone H2A type 1-B/E	protein	104	57% helix, 6% strand	P04908
H	Histone H2B type 1-a	protein	92	74% helix, 4% strand	Q96A08
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 5 copies · chains 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.81	0.83	84	empty
2	774	0.79	0.83	84	empty
3	469	0.75	0.84	47	empty
4	926	0.73	0.78	69	empty
5	810	0.70	0.77	58	MN

Interfaces

36 interfaces between chains.

I–J · 6426 Å² buried · 516 hydrogen bonds · nucleic-nucleic
E–F · 2638 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2620 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 2585 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2557 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3WKJ · The nucleosome containing human TSH2B · the same entry in another collection · chain G against G, 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 0.97

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 Q96A08
Elsewhere: RCSB PDB 3WKJ · PDBe 3WKJ · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt Q96A08

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