Research workbench

NUA4 bound to the nucleosome

Analyse NUA4 bound to the nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VVZ
Type: protein + DNA
Length: 7,030 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromatin modification-related protein EAF6; Chromatin modification-related protein YNG2…
UniProt: P47128, P38806, P43572, Q08649, Q06337, P80428, P60010, P53201, P38811
Ligands: ATP, CMC, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 20 distinct chains · 55% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Y	Chromatin modification-related protein EAF6	protein	46	96% helix, 0% strand	P47128
V	Chromatin modification-related protein YNG2	protein	113	89% helix, 0% strand	P38806
T	Enhancer of polycomb-like protein 1	protein	274	55% helix, 1% strand	P43572
O	Histone H3	protein	96	67% helix, 4% strand	—
Q	Histone H4	protein	80	64% helix, 9% strand	—
S, N	Histone H2A	protein	106	57% helix, 7% strand	—
U	Histone H2B	protein	92	75% helix, 4% strand	—
A	Histone H3	protein	94	68% helix, 4% strand	—
B	Histone H4	protein	87	61% helix, 8% strand	—
D	Histone H2B	protein	93	75% helix, 4% strand	—
P	Histone acetyltransferase ESA1	protein	270	37% helix, 22% strand	Q08649
W	DNA (207-mer)	dna	180	—	—
I	DNA (207-mer)	dna	179	—	—
X	EPL1 arginine anchor	protein	9	0% helix, 0% strand	—
E	Chromatin modification-related protein EAF1	protein	415	43% helix, 6% strand	Q06337
F	Actin-related protein 4	protein	414	35% helix, 18% strand	P80428
G	Actin	protein	357	41% helix, 19% strand	P60010
K	SWR1-complex protein 4	protein	237	54% helix, 8% strand	P53201
H	Enhancer of polycomb-like protein 1	protein	269	42% helix, 14% strand	P43572
L	Transcription-associated protein 1	protein	3513	59% helix, 2% strand	P38811

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains F, G
CMC · Carboxymethyl coenzyme *A · ligand · chains B, P
MG · Magnesium ion · metal · 2 copies · chains 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	729	0.89	0.93	101	MG, ATP
2	577	0.88	0.93	84	empty
3	1032	0.87	0.88	111	empty
4	1033	0.87	0.88	122	empty
5	304	0.84	0.94	42	empty

Interfaces

62 interfaces between chains.

W–I · 8054 Å² buried · 658 hydrogen bonds · nucleic-nucleic
E–H · 6318 Å² buried · 68 hydrogen bonds · protein-protein
E–L · 5247 Å² buried · 31 hydrogen bonds · protein-protein
E–K · 4319 Å² buried · 33 hydrogen bonds · protein-protein
T–P · 3217 Å² buried · 62 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7VVZ · NuA4 bound to the nucleosome · the same entry in another collection · chain D against D, 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 P47128
Every structure of UniProt P38806
Every structure of UniProt P43572
Every structure of UniProt Q08649
Every structure of UniProt Q06337
Every structure of UniProt P80428
Every structure of UniProt P60010
Every structure of UniProt P53201
Every structure of UniProt P38811
Elsewhere: RCSB PDB 7VVZ · PDBe 7VVZ · UniProt P47128 · UniProt P38806 · UniProt P43572 · UniProt Q08649 · UniProt Q06337 · UniProt P80428 · UniProt P60010 · UniProt P53201 · UniProt P38811

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