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Crystal structure of yeats domain of AF9 in complex with H3K9BZ peptide

Analyse Crystal structure of yeats domain of AF9 in complex with H3K9BZ peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LS6
Type: protein
Length: 292 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein af-9; 2
UniProt: P42568
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein af-9	protein	138	11% helix, 51% strand	P42568
C, D	2	protein	8	0% helix, 25% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.60	0.77	47	empty
2	131	0.42	0.75	22	empty
3	55	0.28	0.74	14	empty

Interfaces

5 interfaces between chains.

B–C · 623 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 607 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 223 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 116 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 99 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

6LS6 · Crystal Structure of YEATS domain of AF9 in complex with H3K9bz 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 B 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 6LS6 · PDBe 6LS6 · UniProt P42568

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