MolNFT v1 · #138676 · protein
Structure of a protein involved in pyroptosis
5WQT · Gasdermin-D: “Structure of a protein involved in pyroptosis”. X-ray diffraction, 6 pockets (best druggability 0.37). MolNFT v1 #138676 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WQT
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gasdermin-D
- UniProt
- P57764
- Pockets
- 6 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gasdermin-D | protein | 198 | 61% helix, 5% strand | P57764 |
| B | Gasdermin-D | protein | 198 | 63% helix, 4% strand | P57764 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.37 | 0.79 | 15 | empty |
| 2 | 53 | 0.35 | 0.78 | 17 | empty |
| 3 | 80 | 0.32 | 0.73 | 17 | empty |
| 4 | 68 | 0.32 | 0.75 | 22 | empty |
| 5 | 71 | 0.31 | 0.74 | 17 | CIT |
Interfaces
1 interface between chains.
- A–B · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
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 P57764
- Elsewhere: RCSB PDB 5WQT · PDBe 5WQT · UniProt P57764
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