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Crystal structure of nucleosome core particle composed of the widom 601 DNA sequence (orientation 1)

Analyse Crystal structure of nucleosome core particle composed of the widom 601 DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LZ0
Type: protein + DNA
Length: 1,041 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; DNA (145-mer)
UniProt: P84233, P62799, Q6AZJ8, P02281
Ligands: MN, CL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	97	66% helix, 4% strand	P84233
B	Histone H4	protein	83	60% helix, 8% strand	P62799
C	Histone H2A	protein	103	56% helix, 6% strand	Q6AZJ8
D	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
E	Histone H3.2	protein	97	65% helix, 4% strand	P84233
F	Histone H4	protein	78	65% helix, 8% strand	P62799
G	Histone H2A	protein	105	54% helix, 7% strand	Q6AZJ8
H	Histone H2B 1.1	protein	93	75% helix, 4% strand	P02281
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains A, B, I, J
CL · Chloride ion · ion · 2 copies · chains C, D, J, 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	519	0.78	0.85	60	empty
2	628	0.77	0.83	66	empty
3	393	0.76	0.86	47	empty
4	1109	0.75	0.78	68	MN
5	811	0.69	0.76	64	empty

Interfaces

36 interfaces between chains.

I–J · 6593 Å² buried · 700 hydrogen bonds · nucleic-nucleic
C–D · 2689 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2658 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2592 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2567 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3LZ0 · Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence… · the same entry in another collection · chain J against J, TM-score 1.00
P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 3LZ0 · PDBe 3LZ0 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281

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