MolNFT v1 · #149101 · protein + DNA

Class 3 : translocated nucleosome

6FQ8 · Histone H3.3C: “Class 3 : translocated nucleosome”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #149101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FQ8
Type: protein + DNA
Length: 1,038 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3C; Histone H4; Histone H2A; Histone H2B; DNA (147-mer)
UniProt: P02302, P62799, Q6AZJ8, A0A1L8FQ56
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 9 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.3C	protein	95	66% helix, 4% strand	P02302
B	Histone H4	protein	84	64% helix, 7% strand	P62799
C	Histone H2A	protein	105	56% helix, 6% strand	Q6AZJ8
D, H	Histone H2B	protein	89	78% helix, 4% strand	A0A1L8FQ56
E	Histone H3.3C	protein	93	68% helix, 4% strand	P02302
F	Histone H4	protein	83	63% helix, 7% strand	P62799
G	Histone H2A	protein	106	54% helix, 6% strand	Q6AZJ8
I	DNA (147-mer)	dna	147	—	—
J	DNA (147-mer)	dna	147	—	—

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	1096	0.85	0.86	142	empty
2	356	0.78	0.88	53	empty
3	573	0.71	0.80	59	empty
4	901	0.68	0.74	69	empty
5	529	0.65	0.77	33	empty

Interfaces

37 interfaces between chains.

I–J · 6820 Å² buried · 746 hydrogen bonds · nucleic-nucleic
G–H · 2548 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2466 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2451 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2412 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6FQ8 · Class 3 : translocated nucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P02302 · AlphaFold monomer V2.0 prediction for histone H3.3C (P02302) · a predicted model of the same protein · chain E against A, TM-score 0.90

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 P02302
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt A0A1L8FQ56
Elsewhere: RCSB PDB 6FQ8 · PDBe 6FQ8 · UniProt P02302 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQ56

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