MolNFT v1 · #176100 · protein + DNA

The mouse nucleosome structure containing H3MM18

7DBH · Histone H3MM18: “The mouse nucleosome structure containing H3MM18”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #176100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DBH
Type: protein + DNA
Length: 949 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3MM18; Histone H4; Histone H2A type 1-B; Histone H2B type 3-a; DNA (126-mer)
UniProt: P62806, C0HKE1, Q9D2U9
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 10 distinct chains · 68% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3MM18	protein	78	65% helix, 5% strand	—
B	Histone H4	protein	82	65% helix, 7% strand	P62806
C	Histone H2A type 1-B	protein	94	60% helix, 6% strand	C0HKE1
D	Histone H2B type 3-a	protein	92	76% helix, 4% strand	Q9D2U9
E	Histone H3MM18	protein	85	73% helix, 5% strand	—
F	Histone H4	protein	77	66% helix, 8% strand	P62806
G	Histone H2A type 1-B	protein	96	61% helix, 6% strand	C0HKE1
H	Histone H2B type 3-a	protein	93	74% helix, 4% strand	Q9D2U9
I	DNA (126-mer)	dna	126	—	—
J	DNA (126-mer)	dna	126	—	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.80	0.83	78	empty
2	310	0.75	0.87	40	empty
3	240	0.69	0.86	34	empty
4	293	0.68	0.83	40	empty
5	721	0.67	0.75	55	empty

Interfaces

37 interfaces between chains.

I–J · 5688 Å² buried · 600 hydrogen bonds · nucleic-nucleic
G–H · 2583 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2533 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 2279 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2272 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7DBH · The mouse nucleosome structure containing H3mm18 · the same entry in another collection · chain J against J, TM-score 1.00
P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain F 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 P62806
Every structure of UniProt C0HKE1
Every structure of UniProt Q9D2U9
Elsewhere: RCSB PDB 7DBH · PDBe 7DBH · UniProt P62806 · UniProt C0HKE1 · UniProt Q9D2U9

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