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Crystal structure of the poplar glutathione peroxidase 5 in the oxidized form

Analyse Crystal structure of the poplar glutathione peroxidase 5 in the oxidized form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P5R
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutathione peroxidase 5
EC: 1.11.1.-
UniProt: A3FNZ8
Ligands: CA
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutathione peroxidase 5 (EC 1.11.1.-)	protein	164	25% helix, 22% strand	A3FNZ8

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.49	0.79	28	empty
2	104	0.34	0.73	23	empty
3	87	0.33	0.74	26	CA

Interfaces

1 interface between chains.

A–B · 858 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2P5R · Crystal structure of the poplar glutathione peroxidase 5 in the oxidized form · the same entry in another collection · chain A 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 A3FNZ8
Elsewhere: RCSB PDB 2P5R · PDBe 2P5R · UniProt A3FNZ8

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