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Schizosaccharomyces pombe dj-1

Analyse Schizosaccharomyces pombe dj-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QYT
Type: protein
Length: 760 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein C22E12.03C
UniProt: Q10356
Ligands: MG
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uncharacterized protein C22E12.03C	protein	190	44% helix, 22% strand	Q10356

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains B, C, D
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	469	0.68	0.79	54	EDO
2	72	0.56	0.87	23	empty
3	66	0.54	0.87	23	empty

Interfaces

4 interfaces between chains.

A–B · 1352 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1338 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 159 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

4QYT · Schizosaccharomyces pombe DJ-1 · the same entry in another collection · chain D against D, TM-score 1.00
Q10356 · AlphaFold monomer V2.0 prediction for glutathione-independent glyoxalase dj-1 (Q10356) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 Q10356
Elsewhere: RCSB PDB 4QYT · PDBe 4QYT · UniProt Q10356

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