MolNFT v1 · #123107 · protein

Crystal structure of the NUA4 core complex

5J9W · Histone acetyltransferase ESA1: “Crystal structure of the NUA4 core complex”. X-ray diffraction, 1 ligand (ACO), 20 pockets (best druggability 0.81). MolNFT v1 #123107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J9W
Type: protein
Length: 2,221 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone acetyltransferase ESA1; Chromatin modification-related protein EAF6; Enhancer of…
EC: 2.3.1.48
UniProt: Q08649, P47128, P43572, P38806
Ligands: ACO
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 59% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A, I	Histone acetyltransferase ESA1 (EC 2.3.1.48)	protein	278	37% helix, 23% strand	Q08649
F	Chromatin modification-related protein EAF6	protein	68	72% helix, 0% strand	P47128
G	Enhancer of polycomb-like protein 1	protein	275	56% helix, 2% strand	P43572
H	Chromatin modification-related protein YNG2	protein	118	85% helix, 0% strand	P38806
B	Chromatin modification-related protein EAF6	protein	74	74% helix, 0% strand	P47128
C	Enhancer of polycomb-like protein 1	protein	267	57% helix, 1% strand	P43572
D, L	Chromatin modification-related protein YNG2	protein	119	84% helix, 0% strand	P38806
J	Chromatin modification-related protein EAF6	protein	70	71% helix, 0% strand	P47128
K	Enhancer of polycomb-like protein 1	protein	277	56% helix, 2% strand	P43572

Ligands and binding sites

ACO · Acetyl coenzyme *A · ligand · 2 copies · chains E, 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	742	0.81	0.85	77	empty
2	856	0.79	0.81	67	empty
3	772	0.76	0.81	83	empty
4	510	0.72	0.81	55	empty
5	327	0.72	0.85	36	empty

Interfaces

23 interfaces between chains.

I–K · 3183 Å² buried · 57 hydrogen bonds · protein-protein
E–G · 3098 Å² buried · 62 hydrogen bonds · protein-protein
C–D · 2999 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 2960 Å² buried · 61 hydrogen bonds · protein-protein
G–H · 2957 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (acetylation).

Compared structures

5J9W · Crystal structure of the NuA4 core complex · the same entry in another collection · chain L against L, 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 Q08649
Every structure of UniProt P47128
Every structure of UniProt P43572
Every structure of UniProt P38806
Elsewhere: RCSB PDB 5J9W · PDBe 5J9W · UniProt Q08649 · UniProt P47128 · UniProt P43572 · UniProt P38806

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