MolNFT v1 · #153828 · protein + DNA

Crystal structure of the human nucleosome phased with 16 selenium atoms

6JR1 · Histone H3.1: “Crystal structure of the human nucleosome phased with 16 selenium atoms”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.76). MolNFT v1 #153828 on GenesisL1: 3D structure, binding sites and…

PDB: 6JR1
Type: protein + DNA
Length: 1,047 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 (146-mer)
UniProt: P68431, P62805, P04908, P06899
Ligands: MN, CL
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 9 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	96	67% helix, 4% strand	P68431
B	Histone H4	protein	78	64% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	108	56% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	93	75% helix, 4% strand	P06899
E	Histone H3.1	protein	98	65% helix, 4% strand	P68431
F	Histone H4	protein	85	59% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	92	76% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains E, 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	307	0.76	0.88	44	empty
2	201	0.73	0.89	35	empty
3	222	0.68	0.85	37	empty
4	221	0.65	0.84	37	empty
5	139	0.65	0.87	24	empty

Interfaces

34 interfaces between chains.

I–J · 6445 Å² buried · 499 hydrogen bonds · nucleic-nucleic
E–F · 2660 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2629 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2584 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2567 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

6JR1 · Crystal structure of the human nucleosome phased with 16 selenium atoms · 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 6JR1 · PDBe 6JR1 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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