MolNFT v1 · #69186 · protein
Crystal structure of the human pdi-peroxidase
3KIJ · Probable glutathione peroxidase 8: “Crystal structure of the human pdi-peroxidase”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.62). MolNFT v1 #69186 on GenesisL1: 3D structure, binding sites and pockets in…
- 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.
| Volume (ų) | 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 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.