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Crystal structure of AF9 yeats domain in complex with H4K8ACK12AC peptide

Analyse Crystal structure of AF9 yeats domain in complex with H4K8ACK12AC peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EID
Type: protein
Length: 297 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein af-9; Histone H4
UniProt: P42568
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein af-9	protein	138	9% helix, 51% strand	P42568
B	Protein af-9	protein	139	11% helix, 50% strand	P42568
C, D	Histone H4	protein	10	0% helix, 10% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.31	0.75	15	empty

Interfaces

4 interfaces between chains.

A–C · 507 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 506 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 427 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 291 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (acetylation).

Compared structures

7EID · Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide · the same entry in another collection · chain A against A, TM-score 1.00
P42568 · AlphaFold monomer V2.0 prediction for protein af-9 (P42568) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P42568
Elsewhere: RCSB PDB 7EID · PDBe 7EID · UniProt P42568

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