MolNFT v1 · #114133 · protein + DNA

The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.

5B32 · Histone H3.3: “The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.82). MolNFT v1 #114133 on GenesisL1: 3D structure, binding sites and…

PDB: 5B32
Type: protein + DNA
Length: 1,044 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; Histone H2A.Z…
UniProt: P84243, P62805, P04908, P06899, P0C0S5
Ligands: MN, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.3	protein	97	66% helix, 4% strand	P84243
B	Histone H4	protein	78	63% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	108	54% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	93	73% helix, 4% strand	P06899
E	Histone H3.3	protein	98	64% helix, 4% strand	P84243
F	Histone H4	protein	83	60% helix, 8% strand	P62805
G	Histone H2A.Z	protein	104	54% helix, 6% strand	P0C0S5
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 10 copies · chains C, D, E, F, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H

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	856	0.82	0.84	80	empty
2	485	0.74	0.83	62	empty
3	447	0.73	0.83	44	empty
4	196	0.71	0.89	33	empty
5	649	0.70	0.78	68	MN

Interfaces

37 interfaces between chains.

I–J · 6486 Å² buried · 623 hydrogen bonds · nucleic-nucleic
C–D · 2654 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 2635 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 2605 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2532 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5B32 · The crystal structure of the heterotypic H2AZ/H2A nucleosome with 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 A against A, TM-score 0.99

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 P84243
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Every structure of UniProt P0C0S5
Elsewhere: RCSB PDB 5B32 · PDBe 5B32 · UniProt P84243 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P0C0S5

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