MolNFT v1 · #71523 · protein + DNA

Binding of rubidium ions to the nucleosome core particle

3MGR · Histone H3.2: “Binding of rubidium ions to the nucleosome core particle”. X-ray diffraction, 3 ligands (MN, RB, CL), 20 pockets (best druggability 0.81). MolNFT v1 #71523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MGR
Type: protein + DNA
Length: 1,066 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (147-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: MN, RB, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	99	65% helix, 4% strand	P84233
B	Histone H4	protein	79	58% helix, 8% strand	P62799
C	Histone H2A	protein	104	57% helix, 7% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	99	71% helix, 4% strand	P02281
F	Histone H4	protein	87	57% helix, 8% strand	P62799
G	Histone H2A	protein	106	56% helix, 6% strand	Q6AZJ8
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
RB · Rubidium ion · metal · 5 copies · chains D, H, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I

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

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	542	0.81	0.87	62	empty
2	303	0.77	0.89	37	empty
3	368	0.76	0.87	45	empty
4	910	0.74	0.78	101	MN, RB
5	541	0.65	0.77	41	empty

Interfaces

36 interfaces between chains.

I–J · 6585 Å² buried · 666 hydrogen bonds · nucleic-nucleic
E–F · 2684 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2666 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2651 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2544 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3MGR · Binding of Rubidium ions to the Nucleosome Core Particle · the same entry in another collection · chain J against J, TM-score 1.00
P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A 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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Elsewhere: RCSB PDB 3MGR · PDBe 3MGR · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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