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Crystal structure of unusual nucleosome

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

PDB: 5GSE
Type: protein + DNA
Length: 1,771 residues
Chains: 16
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 (250-mer)
UniProt: P68431, P62805, P04908, P06899
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 15 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, O	Histone H3.1	protein	96	67% helix, 4% strand	P68431
B	Histone H4	protein	82	57% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	102	58% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
E	Histone H3.1	protein	97	68% helix, 4% strand	P68431
F	Histone H4	protein	79	62% helix, 9% strand	P62805
G	Histone H2A type 1-B/E	protein	109	54% helix, 6% strand	P04908
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I	DNA (250-mer)	dna	245	—	—
J	DNA (250-mer)	dna	245	—	—
K	Histone H3.1	protein	88	69% helix, 5% strand	P68431
L	Histone H4	protein	69	68% helix, 6% strand	P62805
M	Histone H2A type 1-B/E	protein	106	57% helix, 7% strand	P04908
N	Histone H2B type 1-J	protein	93	74% helix, 4% strand	P06899
P	Histone H4	protein	81	62% helix, 9% strand	P62805

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	1157	0.83	0.84	125	empty
2	417	0.77	0.86	49	empty
3	968	0.75	0.78	68	empty
4	566	0.72	0.80	54	empty
5	841	0.70	0.77	59	empty

Interfaces

59 interfaces between chains.

I–J · 11020 Å² buried · 871 hydrogen bonds · nucleic-nucleic
O–P · 2622 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2612 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2606 Å² buried · 28 hydrogen bonds · protein-protein
M–N · 2547 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

5GSE · Crystal structure of unusual nucleosome · 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 5GSE · PDBe 5GSE · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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