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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: 1P3I
Type: protein + DNA
Length: 1,048 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 0.75

Structure

x-ray diffraction · 8 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146BP human alpha-satellite DNA fragment	dna	146	—	—
A	Histone H3	protein	98	62% helix, 4% strand	Q7ZT64
B, F	Histone H4	protein	79	63% helix, 9% strand	P62799
C	Histone H2A	protein	103	58% helix, 7% strand	Q7ZT66
D	Histone H2B	protein	95	74% helix, 4% strand	P02281
E	Histone H3	protein	104	63% helix, 4% strand	Q7ZT64
G	Histone H2A	protein	104	57% helix, 7% strand	Q7ZT66
H	Histone H2B	protein	94	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	527	0.75	0.83	56	empty
2	366	0.75	0.86	46	empty
3	382	0.74	0.85	48	empty
4	733	0.69	0.77	51	empty
5	561	0.67	0.78	47	empty

Interfaces

36 interfaces between chains.

I–J · 6419 Å² buried · 508 hydrogen bonds · nucleic-nucleic
C–D · 2653 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2632 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2587 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2487 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

1P3I · Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants · the same entry in another collection · chain I against I, 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 1P3I · PDBe 1P3I · UniProt Q7ZT64 · UniProt P62799 · UniProt Q7ZT66 · UniProt P02281

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