MolNFT v1 · #139647 · protein + DNA

The mouse nucleosome structure containing H2A, H2B TYPE3-a, H3MM7, and H4

5XM1 · Histone H3MM7: “The mouse nucleosome structure containing H2A, H2B TYPE3-a, H3MM7, and H4”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #139647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XM1
Type: protein + DNA
Length: 1,042 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3MM7; Histone H4; Histone H2A type 1-B; Histone H2B type 3-a; DNA (146-mer)
UniProt: P62806, C0HKE1, Q9D2U9
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3MM7	protein	97	65% helix, 4% strand	—
B	Histone H4	protein	78	63% helix, 8% strand	P62806
C	Histone H2A type 1-B	protein	105	55% helix, 6% strand	C0HKE1
D	Histone H2B type 3-a	protein	94	70% helix, 4% strand	Q9D2U9
E	Histone H3MM7	protein	98	65% helix, 4% strand	—
F	Histone H4	protein	83	59% helix, 7% strand	P62806
G	Histone H2A type 1-B	protein	104	57% helix, 6% strand	C0HKE1
H	Histone H2B type 3-a	protein	91	75% helix, 4% strand	Q9D2U9
I, J	DNA (146-mer)	dna	146	—	—

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	796	0.81	0.84	63	empty
2	433	0.76	0.86	44	empty
3	444	0.75	0.85	46	empty
4	762	0.68	0.76	60	empty
5	553	0.66	0.77	54	empty

Interfaces

35 interfaces between chains.

I–J · 6436 Å² buried · 566 hydrogen bonds · nucleic-nucleic
C–D · 2656 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2628 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2623 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2502 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5XM1 · The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 · 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 B against A, TM-score 0.98

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 5XM1 · PDBe 5XM1 · UniProt P62806 · UniProt C0HKE1 · UniProt Q9D2U9

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