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Crystal structure of the human nucleosome containing 6-4PP (outside)

Analyse Crystal structure of the human nucleosome containing 6-4PP (outside) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YM6
Type: protein + DNA
Length: 1,048 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; 145-mer DNA
UniProt: P68431, P62805, P04908, P06899
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	65% helix, 4% strand	P68431
B	Histone H4	protein	78	59% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	108	54% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	96	71% helix, 4% strand	P06899
E	Histone H3.1	protein	99	64% helix, 4% strand	P68431
F	Histone H4	protein	84	54% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	56% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	92	74% helix, 4% strand	P06899
I, J	145-mer DNA	dna	145	—	—

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	829	0.81	0.84	70	empty
2	501	0.77	0.85	47	empty
3	453	0.75	0.84	48	empty
4	756	0.73	0.79	58	empty
5	272	0.69	0.85	33	empty

Interfaces

36 interfaces between chains.

I–J · 6561 Å² buried · 678 hydrogen bonds · nucleic-nucleic
E–F · 2658 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2636 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2633 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2571 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4YM6 · Crystal structure of the human nucleosome containing 6-4PP (outside) · 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 4YM6 · PDBe 4YM6 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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