Research workbench

Yeats in complex with histone H3

Analyse Yeats in complex with histone H3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VNB
Type: protein
Length: 515 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yeats domain-containing protein 4; H3K23ACK27AC peptide
UniProt: O95619
Ligands: SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yeats domain-containing protein 4	protein	129	4% helix, 51% strand	O95619
B, C	Yeats domain-containing protein 4	protein	127	4% helix, 52% strand	O95619
D	Yeats domain-containing protein 4	protein	122	2% helix, 54% strand	O95619
K	H3K23ACK27AC peptide	protein	10	0% helix, 10% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, C, B
EDO · 1,2-ethanediol · additive · 7 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	740	0.71	0.77	71	empty
2	312	0.53	0.74	31	SO4
3	117	0.37	0.74	18	empty
4	100	0.33	0.72	18	EDO

Interfaces

8 interfaces between chains.

A–C · 700 Å² buried · 10 hydrogen bonds · protein-protein
D–K · 451 Å² buried · 5 hydrogen bonds · protein-protein
B–K · 424 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 240 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 168 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (acetylation).

Compared structures

5VNB · YEATS in complex with histone H3 · the same entry in another collection · chain K against K, TM-score 1.00
O95619 · AlphaFold monomer V2.0 prediction for yeats domain-containing protein 4 (O95619) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O95619
Elsewhere: RCSB PDB 5VNB · PDBe 5VNB · UniProt O95619

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