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Crystal structure of nucleosome core particle assembled with an alpha- satellite sequence containing two ttaaa elements (ncp-TA2)

Analyse Crystal structure of nucleosome core particle assembled with an alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UTA
Type: protein + DNA
Length: 1,055 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; 145-mer DNA
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: MN, CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	97	66% helix, 4% strand	P84233
B	Histone H4	protein	82	61% helix, 9% strand	P62799
C, G	Histone H2A	protein	106	56% helix, 6% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	95	75% helix, 4% strand	P02281
F	Histone H4	protein	87	57% helix, 7% strand	P62799
I	145-mer DNA	dna	145	—	—
J	145-mer DNA	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 17 copies · chains E, F, I, J
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I

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	806	0.79	0.83	80	empty
2	543	0.75	0.83	59	empty
3	340	0.74	0.86	39	empty
4	641	0.71	0.79	69	MN
5	181	0.68	0.88	30	empty

Interfaces

38 interfaces between chains.

I–J · 6542 Å² buried · 617 hydrogen bonds · nucleic-nucleic
E–F · 2631 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2607 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2587 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2570 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3UTA · Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence… · 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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Elsewhere: RCSB PDB 3UTA · PDBe 3UTA · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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