MolNFT v1 · #14370 · protein
Crystal structure of caspase-1 from spodoptera frugiperda
1M72: “Crystal structure of caspase-1 from spodoptera frugiperda”. X-ray diffraction, 2 ligands (ACE, 0QE), 4 pockets (best druggability 0.74). MolNFT v1 #14370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1M72
- Type
- protein
- Length
- 759 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-1; ACE-asp-glu-val-asp-chloromethylketone
- EC
- 3.4.22.36
- UniProt
- P89116
- Ligands
- ACE, 0QE
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-1 (EC 3.4.22.36) | protein | 247 | 26% helix, 27% strand | P89116 |
| D, E, F | ACE-asp-glu-val-asp-chloromethylketone | protein | 4 | 0% helix, 50% strand | — |
| B | Caspase-1 (EC 3.4.22.36) | protein | 248 | 26% helix, 27% strand | P89116 |
| C | Caspase-1 (EC 3.4.22.36) | protein | 252 | 26% helix, 21% strand | P89116 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, D, B, E, C, F
- 0QE · Chloromethane · ion · 3 copies · chains A, D, B, E, C, F
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.74 | 0.79 | 55 | EDO |
| 2 | 97 | 0.42 | 0.78 | 15 | empty |
| 3 | 69 | 0.29 | 0.73 | 16 | 0QE |
| 4 | 70 | 0.29 | 0.73 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2583 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 467 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 455 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
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 P89116
- Elsewhere: RCSB PDB 1M72 · PDBe 1M72 · UniProt P89116
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