MolNFT v1 · #143368 · protein

Crystal structure of the YAF9 yeats domain bound to H3K27AC

6AXJ · Protein af-9 homolog: “Crystal structure of the YAF9 yeats domain bound to H3K27AC”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.71). MolNFT v1 #143368 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6AXJ
Type: protein
Length: 589 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein af-9 homolog; Aly-ser-ala-pro-ala
UniProt: P53930
Ligands: SO4
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein af-9 homolog	protein	143	10% helix, 48% strand	P53930
C, B, D	Protein af-9 homolog	protein	142	11% helix, 47% strand	P53930
G, E, H, F	Aly-ser-ala-pro-ala	protein	5	0% helix, 20% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, G, C, D, H, F
GOL · Glycerol · additive · 10 copies · chains A, C, B, D

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.71	0.76	94	SO4
2	186	0.67	0.86	32	SO4
3	291	0.52	0.74	41	empty

Interfaces

14 interfaces between chains.

C–F · 395 Å² buried · 6 hydrogen bonds · protein-protein
B–G · 393 Å² buried · 5 hydrogen bonds · protein-protein
D–H · 389 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 387 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 303 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (acetylation).

Compared structures

6AXJ · Crystal structure of the Yaf9 YEATS domain bound to H3K27ac · the same entry in another collection · chain F against F, TM-score 1.00
P53930 · AlphaFold monomer V2.0 prediction for protein af-9 homolog (P53930) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P53930
Elsewhere: RCSB PDB 6AXJ · PDBe 6AXJ · UniProt P53930

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