Research workbench
Crystal structure of calcium-bound protease core of calpain II reveals the basis for intrinsic inactivation
Analyse Crystal structure of calcium-bound protease core of calpain II reveals the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MDW
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain II, catalytic subunit
- EC
- 3.4.22.17
- UniProt
- Q07009
- Ligands
- CA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain II, catalytic subunit (EC 3.4.22.17) | protein | 319 | 30% helix, 24% strand | Q07009 |
| B | Calpain II, catalytic subunit (EC 3.4.22.17) | protein | 318 | 31% helix, 23% strand | Q07009 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.70 | 0.76 | 111 | empty |
| 2 | 54 | 0.56 | 0.89 | 21 | empty |
| 3 | 52 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1MDW · Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07009 · AlphaFold monomer V2.0 prediction for calpain-2 catalytic subunit (Q07009) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q07009
- Elsewhere: RCSB PDB 1MDW · PDBe 1MDW · UniProt Q07009
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.