MolNFT v1 · #17770 · protein + DNA

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

1P3K · Palindromic 146BP human alpha-satellite DNA fragment: “Crystallographic studies of nucleosome core particles containing histone 'sin' mutants”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #17770 on GenesisL1…

PDB: 1P3K
Type: protein + DNA
Length: 1,046 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 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146BP human alpha-satellite DNA fragment	dna	146	—	—
A	Histone H3	protein	97	65% helix, 4% strand	Q7ZT64
B	Histone H4	protein	79	58% helix, 8% strand	P62799
C	Histone H2A	protein	106	58% helix, 7% strand	Q7ZT66
D	Histone H2B	protein	92	76% helix, 4% strand	P02281
E	Histone H3	protein	99	62% helix, 4% strand	Q7ZT64
F	Histone H4	protein	81	62% helix, 9% strand	P62799
G	Histone H2A	protein	106	55% helix, 6% strand	Q7ZT66
H	Histone H2B	protein	94	73% helix, 4% strand	P02281

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.84	0.85	107	empty
2	897	0.81	0.83	91	empty
3	597	0.67	0.77	51	empty
4	493	0.66	0.78	42	empty
5	642	0.66	0.76	60	empty

Interfaces

37 interfaces between chains.

I–J · 6269 Å² buried · 534 hydrogen bonds · nucleic-nucleic
G–H · 2654 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2648 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2570 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 2550 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1P3K · 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 1P3K · PDBe 1P3K · UniProt Q7ZT64 · UniProt P62799 · UniProt Q7ZT66 · UniProt P02281

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