MolNFT v1 · #16019 · protein
Structure of casp-3 with tethered salicylate
1NME · Caspase-3: “Structure of casp-3 with tethered salicylate”. X-ray diffraction, 2 ligands (158, 159), 1 pocket (best druggability 0.35). MolNFT v1 #16019 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NME
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3
- EC
- 3.4.22.-
- UniProt
- P42574
- Ligands
- 158, 159
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 (EC 3.4.22.-) | protein | 146 | 26% helix, 29% strand | P42574 |
| B | Caspase-3 (EC 3.4.22.-) | protein | 92 | 34% helix, 17% strand | P42574 |
Ligands and binding sites
- 158 · 3-(2-mercapto-acetylamino)-4-oxo-pentanoic acid · ligand · chains A, B
- 159 · 2-hydroxy-5-(2-mercapto-ethylsulfamoyl)-benzoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.35 | 0.75 | 17 | 158 |
Interfaces
1 interface between chains.
- A–B · 2232 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 P42574
- Elsewhere: RCSB PDB 1NME · PDBe 1NME · UniProt P42574
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