MolNFT v1 · #114114 · protein + DNA

Human nucleosome containing cpg methylated DNA

5B2J · Histone H3.1: “Human nucleosome containing cpg methylated DNA”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.79). MolNFT v1 #114114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B2J
Type: protein + DNA
Length: 1,059 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
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.1	protein	99	64% helix, 4% strand	P68431
B	Histone H4	protein	82	56% 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	72% helix, 4% strand	P06899
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	94	74% helix, 4% strand	P06899
I, J	DNA (146-mer)	dna	146	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 7 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	695	0.79	0.83	71	empty
2	460	0.77	0.85	54	empty
3	415	0.77	0.86	57	empty
4	839	0.73	0.78	57	empty
5	290	0.70	0.85	38	empty

Interfaces

36 interfaces between chains.

I–J · 6478 Å² buried · 596 hydrogen bonds · nucleic-nucleic
C–D · 2606 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2586 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2585 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2555 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

5B2J · Human nucleosome containing CpG methylated DNA · 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 5B2J · PDBe 5B2J · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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