MolNFT v1 · #6228 · protein + DNA

2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z

1F66 · Palindromic 146 base pair DNA fragment: “2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.78). MolNFT v1 #6228 on…

PDB: 1F66
Type: protein + DNA
Length: 1,061 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palindromic 146 base pair DNA fragment; Histone H3; Histone H4; Histone H2A.Z; Histone H2B
UniProt: Q7ZT64, P62806, P17317, P02281
Ligands: MN
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146 base pair DNA fragment	dna	146	—	—
A	Histone H3	protein	100	64% helix, 4% strand	Q7ZT64
B	Histone H4	protein	80	63% helix, 8% strand	P62806
C	Histone H2A.Z	protein	103	57% helix, 6% strand	P17317
D, H	Histone H2B	protein	95	74% helix, 4% strand	P02281
E	Histone H3	protein	103	61% helix, 4% strand	Q7ZT64
F	Histone H4	protein	86	58% helix, 7% strand	P62806
G	Histone H2A.Z	protein	107	51% helix, 6% strand	P17317

Ligands and binding sites

MN · Manganese (II) ion · metal · 15 copies · chains I, J, C, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	725	0.78	0.83	86	empty
2	355	0.71	0.83	49	empty
3	563	0.68	0.78	51	empty
4	594	0.66	0.77	36	empty
5	565	0.65	0.77	29	empty

Interfaces

34 interfaces between chains.

I–J · 6379 Å² buried · 526 hydrogen bonds · nucleic-nucleic
G–H · 2644 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2593 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2591 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2531 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

1F66 · 2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z · the same entry in another collection · chain H against H, TM-score 1.00
P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P62806
Every structure of UniProt P17317
Every structure of UniProt P02281
Elsewhere: RCSB PDB 1F66 · PDBe 1F66 · UniProt Q7ZT64 · UniProt P62806 · UniProt P17317 · UniProt P02281

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