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Crystallographic studies of nucleosome core particles containing histone 'sin' mutants

Analyse Crystallographic studies of nucleosome core particles containing histone 'sin'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P3F
Type: protein + DNA
Length: 1,049 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palindromic 146BP human alpha-satellite DNA fragment; Histone H3; Histone H4; Histone…
UniProt: Q7ZT64, P62799, Q7ZT66, P02281
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146BP human alpha-satellite DNA fragment	dna	146	—	—
A, E	Histone H3	protein	99	64% helix, 4% strand	Q7ZT64
B	Histone H4	protein	80	64% helix, 9% strand	P62799
C	Histone H2A	protein	104	58% helix, 6% strand	Q7ZT66
D	Histone H2B	protein	91	76% helix, 4% strand	P02281
F	Histone H4	protein	82	61% helix, 7% strand	P62799
G	Histone H2A	protein	107	54% helix, 7% strand	Q7ZT66
H	Histone H2B	protein	95	73% helix, 4% strand	P02281

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	828	0.79	0.83	90	empty
2	348	0.75	0.86	47	empty
3	333	0.73	0.86	46	empty
4	659	0.66	0.76	42	empty
5	340	0.65	0.81	39	empty

Interfaces

37 interfaces between chains.

I–J · 6327 Å² buried · 580 hydrogen bonds · nucleic-nucleic
C–D · 2631 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2579 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2541 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2526 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1P3F · Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants · the same entry in another collection · chain C against C, 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 Q7ZT64
Every structure of UniProt P62799
Every structure of UniProt Q7ZT66
Every structure of UniProt P02281
Elsewhere: RCSB PDB 1P3F · PDBe 1P3F · UniProt Q7ZT64 · UniProt P62799 · UniProt Q7ZT66 · UniProt P02281

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