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Crystal structure of GAS41

Analyse Crystal structure of GAS41 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y8V
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yeats domain-containing protein 4
UniProt: O95619
Ligands: MG
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C	Yeats domain-containing protein 4	protein	134	5% helix, 48% strand	O95619
D	Yeats domain-containing protein 4	protein	130	2% helix, 50% strand	O95619

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains B, A, C, D

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

Pockets

4 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	738	0.71	0.78	77	empty
2	219	0.49	0.75	33	empty
3	159	0.43	0.74	25	empty
4	70	0.32	0.74	17	empty

Interfaces

5 interfaces between chains.

A–D · 520 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 501 Å² buried · 4 hydrogen bonds · protein-protein
B–A · 497 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 54 Å² buried · 1 hydrogen bond · protein-protein
B–D · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5Y8V · Crystal structure of GAS41 · 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 D 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 O95619
Elsewhere: RCSB PDB 5Y8V · PDBe 5Y8V · UniProt O95619

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