Research workbench

Crystal structure of the heterotypic nucleosome containing human cenp- a and H3.3

Analyse Crystal structure of the heterotypic nucleosome containing human cenp- a and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WTP
Type: protein + DNA
Length: 1,041 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3-like centromeric protein a; Histone H4; Histone H2A type 1-B/E; Histone H2B…
UniProt: P49450, P62805, P04908, P06899, P84243
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3-like centromeric protein a	protein	89	71% helix, 4% strand	P49450
B	Histone H4	protein	78	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	107	57% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	94	70% helix, 4% strand	P06899
E	Histone H3.3	protein	100	66% helix, 4% strand	P84243
F	Histone H4	protein	85	59% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	103	59% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	93	72% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

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	321	0.75	0.87	49	empty
2	210	0.72	0.88	35	empty
3	660	0.70	0.78	47	empty
4	745	0.69	0.77	55	empty
5	206	0.67	0.85	28	empty

Interfaces

36 interfaces between chains.

I–J · 6480 Å² buried · 682 hydrogen bonds · nucleic-nucleic
E–F · 2643 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2638 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2613 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2513 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3WTP · Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 · the same entry in another collection · chain J against J, TM-score 1.00
P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain E against A, TM-score 0.98
P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain A 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 P49450
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Every structure of UniProt P84243
Elsewhere: RCSB PDB 3WTP · PDBe 3WTP · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P84243

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.