Research workbench

Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming

Analyse Crystal structure of nucleosome core particle in the presence of histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X1V
Type: protein + DNA
Length: 1,063 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (146-mer); Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-a
UniProt: P68431, P62805, P04908, P70696
Ligands: MN, CL
Pockets: 20 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	DNA (146-mer)	dna	146	—	—
A	Histone H3.1	protein	98	64% helix, 4% strand	P68431
B	Histone H4	protein	79	62% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	106	56% helix, 7% strand	P04908
D	Histone H2B type 1-a	protein	99	68% helix, 4% strand	P70696
E	Histone H3.1	protein	99	67% helix, 4% strand	P68431
F	Histone H4	protein	87	57% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	109	54% helix, 6% strand	P04908
H	Histone H2B type 1-a	protein	94	74% helix, 4% strand	P70696

Ligands and binding sites

MN · Manganese (II) ion · metal · 19 copies · chains I, J, D, G, H
CL · Chloride ion · ion · 6 copies · chains I, J, B, C, D

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	623	0.79	0.85	67	empty
2	401	0.76	0.85	53	empty
3	299	0.75	0.88	48	empty
4	723	0.70	0.78	51	empty
5	810	0.70	0.77	57	MN

Interfaces

37 interfaces between chains.

I–J · 6337 Å² buried · 552 hydrogen bonds · nucleic-nucleic
C–D · 2663 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2655 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2624 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2455 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3X1V · Crystal structure of nucleosome core particle in the presence of histone variant involved… · the same entry in another collection · chain H against H, TM-score 1.00
P70696 · AlphaFold monomer V2.0 prediction for histone H2B type 1-a (P70696) · a predicted model of the same protein · chain H against A, TM-score 0.97

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 P70696
Elsewhere: RCSB PDB 3X1V · PDBe 3X1V · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P70696

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