Research workbench
Crystal structure of the human PDI first domain with 9 mutations
Analyse Crystal structure of the human PDI first domain with 9 mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8GDY
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Homo sapiens
- Molecule
- Protein disulfide-isomerase
- EC
- 5.3.4.1
- UniProt
- P07237
- Ligands
- SCN
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · resolution 2.05 · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 118 | 40% helix, 22% strand | P07237 |
| B | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 120 | 38% helix, 22% strand | P07237 |
Ligands and binding sites
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.41 | 0.76 | 25 | empty |
| 2 | 55 | 0.35 | 0.78 | 15 | empty |
| 3 | 73 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 305 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- P07237 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase (P07237) · 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 P07237
- Elsewhere: RCSB PDB 8GDY · PDBe 8GDY · UniProt P07237
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