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The structure of human GPX8

Analyse The structure of human GPX8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CYN
Type: protein
Length: 523 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable glutathione peroxidase 8
EC: 1.11.1.9
UniProt: Q8TED1
Ligands: SO4
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable glutathione peroxidase 8 (EC 1.11.1.9)	protein	174	39% helix, 20% strand	Q8TED1
B	Probable glutathione peroxidase 8 (EC 1.11.1.9)	protein	173	39% helix, 20% strand	Q8TED1
C	Probable glutathione peroxidase 8 (EC 1.11.1.9)	protein	176	41% helix, 19% strand	Q8TED1

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

5 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	280	0.65	0.82	39	SO4
2	128	0.43	0.76	34	SO4
3	117	0.41	0.76	19	empty
4	110	0.41	0.76	15	empty
5	51	0.29	0.75	12	empty

Interfaces

3 interfaces between chains.

A–B · 454 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 446 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 442 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3CYN · The structure of human GPX8 · the same entry in another collection · chain A against A, TM-score 1.00
Q8TED1 · AlphaFold monomer V2.0 prediction for probable glutathione peroxidase 8 (Q8TED1) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q8TED1
Elsewhere: RCSB PDB 3CYN · PDBe 3CYN · UniProt Q8TED1

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