MolNFT v1 · #113878 · protein + DNA

Human nucleosome core particle

5AVB · Histone H3.1: “Human nucleosome core particle”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.76). MolNFT v1 #113878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AVB
Type: protein + DNA
Length: 1,063 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (147-mer)
UniProt: P68431, P62805, P04908, P06899
Ligands: MN
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.1	protein	99	65% helix, 4% strand	P68431
B	Histone H4	protein	82	60% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	106	57% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	97	71% helix, 4% strand	P06899
F	Histone H4	protein	87	57% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	105	57% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	94	74% helix, 4% strand	P06899
I	DNA (147-mer)	dna	147	—	—
J	DNA (147-mer)	dna	147	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 14 copies · chains E, F, I, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	372	0.76	0.87	54	empty
2	530	0.76	0.83	60	empty
3	360	0.76	0.87	47	empty
4	765	0.70	0.77	53	empty
5	678	0.69	0.77	69	empty

Interfaces

35 interfaces between chains.

I–J · 6486 Å² buried · 611 hydrogen bonds · nucleic-nucleic
E–F · 2658 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2625 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2600 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2557 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5AVB · human nucleosome core particle · the same entry in another collection · chain A against A, TM-score 1.00

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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 5AVB · PDBe 5AVB · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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