Research workbench

GAS41 yeats domain in complex with 5

Analyse GAS41 yeats domain in complex with 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JFY
Type: protein
Length: 508 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yeats domain-containing protein 4
UniProt: O95619
Ligands: V91
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Yeats domain-containing protein 4	protein	125	6% helix, 50% strand	O95619
A	Yeats domain-containing protein 4	protein	131	6% helix, 53% strand	O95619
C, D	Yeats domain-containing protein 4	protein	126	5% helix, 52% strand	O95619

Ligands and binding sites

V91 · N-(5-{3-[(2S)-1,3-thiazolidin-2-yl]azetidine-1-carbonyl}thiophen-2-yl)-L-prolinamide · ligand · 4 copies · chains B, A, C, D
EDO · 1,2-ethanediol · additive · 6 copies · chains B, A, C, D
DMS · Dimethyl sulfoxide · additive · chains B, D

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

Pockets

2 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	440	0.74	0.84	47	DMS, EDO
2	301	0.70	0.84	29	EDO

Interfaces

5 interfaces between chains.

A–C · 596 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 575 Å² buried · 12 hydrogen bonds · protein-protein
B–A · 546 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 527 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 451 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7JFY · GAS41 YEATS domain in complex with 5 · the same entry in another collection · chain B against B, 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 C 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 7JFY · PDBe 7JFY · UniProt O95619

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.