MolNFT v1 · #154808 · protein
Caspase-1 P20/P10 C285A in complex with human gsdmd-C domain
6KN0: “Caspase-1 P20/P10 C285A in complex with human gsdmd-C domain”. X-ray diffraction, 8 pockets (best druggability 0.72). MolNFT v1 #154808 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KN0
- Type
- protein
- Length
- 897 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-1; Gasdermin-D
- EC
- 3.4.22.36
- UniProt
- P29466, P57764
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caspase-1 (EC 3.4.22.36) | protein | 167 | 30% helix, 24% strand | P29466 |
| B, D | Caspase-1 (EC 3.4.22.36) | protein | 88 | 27% helix, 24% strand | P29466 |
| E | Gasdermin-D | protein | 195 | 58% helix, 6% strand | P57764 |
| F | Gasdermin-D | protein | 192 | 61% helix, 5% strand | P57764 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.72 | 0.83 | 41 | empty |
| 2 | 245 | 0.60 | 0.80 | 29 | empty |
| 3 | 123 | 0.45 | 0.78 | 20 | empty |
| 4 | 110 | 0.41 | 0.76 | 21 | empty |
| 5 | 61 | 0.35 | 0.78 | 16 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2706 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2663 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 1495 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 625 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6KN0 · caspase-1 P20/P10 C285A in complex with human GSDMD-C domain · the same entry in another collection · chain F against F, TM-score 1.00
- P57764 · AlphaFold monomer V2.0 prediction for gasdermin-D (P57764) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P29466 · AlphaFold monomer V2.0 prediction for caspase-1 (P29466) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P29466
- Every structure of UniProt P57764
- Elsewhere: RCSB PDB 6KN0 · PDBe 6KN0 · UniProt P29466 · UniProt P57764
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