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Crystal structure of the human pdi-peroxidase

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

PDB: 3KIJ
Type: protein
Length: 510 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: 6 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Probable glutathione peroxidase 8 (EC 1.11.1.9)	protein	171	37% helix, 19% strand	Q8TED1
C	Probable glutathione peroxidase 8 (EC 1.11.1.9)	protein	168	36% helix, 19% strand	Q8TED1

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, B, C

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

Pockets

6 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	149	0.62	0.85	22	empty
2	169	0.49	0.77	22	empty
3	128	0.49	0.79	21	empty
4	138	0.48	0.78	18	empty
5	141	0.47	0.77	35	SO4

Interfaces

3 interfaces between chains.

B–C · 476 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 453 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 450 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3KIJ · Crystal structure of the human PDI-peroxidase · 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 A 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 Q8TED1
Elsewhere: RCSB PDB 3KIJ · PDBe 3KIJ · UniProt Q8TED1

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