MolNFT v1 · #111934 · protein + DNA

The nucleosome containing human H3.5

4Z5T · Histone H3.3C: “The nucleosome containing human H3.5”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #111934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z5T
Type: protein + DNA
Length: 1,040 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3C; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
UniProt: Q6NXT2, P62805, P04908, P06899
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.3C	protein	97	68% helix, 4% strand	Q6NXT2
B	Histone H4	protein	83	60% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	105	57% helix, 7% strand	P04908
D, H	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
E	Histone H3.3C	protein	96	67% helix, 4% strand	Q6NXT2
F	Histone H4	protein	79	63% helix, 9% strand	P62805
G	Histone H2A type 1-B/E	protein	104	59% helix, 7% strand	P04908
I, J	DNA (146-mer)	dna	146	—	—

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	796	0.81	0.84	81	empty
2	403	0.73	0.84	45	empty
3	431	0.73	0.83	46	empty
4	747	0.70	0.77	67	empty
5	681	0.69	0.77	42	empty

Interfaces

35 interfaces between chains.

I–J · 6406 Å² buried · 670 hydrogen bonds · nucleic-nucleic
G–H · 2590 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2586 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2577 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2473 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4Z5T · The nucleosome containing human H3.5 · the same entry in another collection · chain J against J, TM-score 1.00
Q6NXT2 · AlphaFold monomer V2.0 prediction for histone H3.3C (Q6NXT2) · a predicted model of the same protein · chain E 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 Q6NXT2
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 4Z5T · PDBe 4Z5T · UniProt Q6NXT2 · UniProt P62805 · UniProt P04908 · UniProt P06899

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