MolNFT v1 · #113972 · protein + DNA

Crystal structure of human nucleosome containing H3.Y

5AY8: “Crystal structure of human nucleosome containing H3.Y”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.76). MolNFT v1 #113972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AY8
Type: protein + DNA
Length: 1,033 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H3.Y; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
UniProt: P62805, P04908, P06899
Ligands: MN, CL
Pockets: 20 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H3.Y	protein	97	65% helix, 4% strand	—
B	Histone H4	protein	78	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	105	56% helix, 7% strand	P04908
D, H	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
E	H3.Y	protein	96	67% helix, 4% strand	—
F	Histone H4	protein	79	62% helix, 9% strand	P62805
G	Histone H2A type 1-B/E	protein	104	55% helix, 7% strand	P04908
I	DNA (146-mer)	dna	145	—	—
J	DNA (146-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains A, B, G, H, I, J
CL · Chloride ion · ion · 2 copies · chains J

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	282	0.76	0.89	43	empty
2	386	0.76	0.86	47	empty
3	1095	0.71	0.75	88	empty
4	303	0.70	0.85	34	empty
5	260	0.69	0.85	41	empty

Interfaces

36 interfaces between chains.

I–J · 6351 Å² buried · 557 hydrogen bonds · nucleic-nucleic
G–H · 2612 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2575 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2503 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2465 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5AY8 · Crystal structure of human nucleosome containing H3.Y · 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 P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 5AY8 · PDBe 5AY8 · UniProt P62805 · UniProt P04908 · UniProt P06899

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