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Crystal structure of AF9 yeats domain in complex with histone H3K9BU

Analyse Crystal structure of AF9 yeats domain in complex with histone H3K9BU in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MIL
Type: protein
Length: 291 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein af-9; Histone H3K9BU
UniProt: P42568

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein af-9	protein	138	11% helix, 53% strand	P42568
B, D	Histone H3K9BU	protein	7	0% helix, 29% strand	—
C	Protein af-9	protein	139	9% helix, 53% strand	P42568

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · chains A
MLI · Malonate ion · additive · chains C

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

Interfaces

3 interfaces between chains.

A–C · 801 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 616 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 565 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

6MIL · Crystal structure of AF9 YEATS domain in complex with histone H3K9bu · 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 0.99

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 6MIL · PDBe 6MIL · UniProt P42568

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