MolNFT v1 · #189344 · protein + DNA

The mouse nucleosome structure containing H3MM18 aided by PL2-6 scfv

7VBM · Histone H3MM18: “The mouse nucleosome structure containing H3MM18 aided by PL2-6 scfv”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #189344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VBM
Type: protein + DNA
Length: 929 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 0.81

Structure

electron microscopy · 9 distinct chains · 66% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3MM18	protein	72	71% helix, 6% strand	—
B	Histone H4	protein	82	62% helix, 7% strand	P62806
C	Histone H2A type 1-B	protein	92	60% helix, 7% strand	C0HKE1
D, H	Histone H2B type 3-a	protein	92	75% helix, 4% strand	Q9D2U9
E	Histone H3MM18	protein	77	70% helix, 5% strand	—
F	Histone H4	protein	77	66% helix, 8% strand	P62806
G	Histone H2A type 1-B	protein	93	57% helix, 6% strand	C0HKE1
I	DNA (126-mer)	dna	126	—	—
J	DNA (126-mer)	dna	126	—	—

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	893	0.81	0.83	82	empty
2	368	0.71	0.83	46	empty
3	288	0.70	0.85	30	empty
4	238	0.66	0.84	36	empty
5	657	0.65	0.75	49	empty

Interfaces

36 interfaces between chains.

I–J · 5634 Å² buried · 421 hydrogen bonds · nucleic-nucleic
G–H · 2600 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2571 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2194 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 2107 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7VBM · The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv · 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 7VBM · PDBe 7VBM · UniProt P62806 · UniProt C0HKE1 · UniProt Q9D2U9

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