MolNFT v1 · #59139 · protein
Structure of M-calpain in complex with calpastatin
3BOW · Calpain-2 catalytic subunit: “Structure of M-calpain in complex with calpastatin”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.85). MolNFT v1 #59139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BOW
- Type
- protein
- Length
- 919 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain-2 catalytic subunit; Calpain small subunit 1; Calpastatin
- EC
- 3.4.22.53
- UniProt
- Q07009, Q64537, P27321
- Ligands
- CA
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-2 catalytic subunit (EC 3.4.22.53) | protein | 680 | 34% helix, 23% strand | Q07009 |
| B | Calpain small subunit 1 (EC 3.4.22.53) | protein | 174 | 60% helix, 6% strand | Q64537 |
| C | Calpastatin | protein | 65 | 42% helix, 5% strand | P27321 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.85 | 0.86 | 88 | empty |
| 2 | 658 | 0.70 | 0.78 | 53 | empty |
| 3 | 354 | 0.64 | 0.79 | 48 | empty |
| 4 | 291 | 0.59 | 0.78 | 41 | CA |
| 5 | 122 | 0.53 | 0.81 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2840 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 591 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3BOW · Structure of M-calpain in complex with Calpastatin · the same entry in another collection · chain A against A, TM-score 1.00
- Q64537 · AlphaFold monomer V2.0 prediction for calpain small subunit 1 (Q64537) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q07009 · AlphaFold monomer V2.0 prediction for calpain-2 catalytic subunit (Q07009) · a predicted model of the same protein · chain A against A, TM-score 0.76
- P27321 · AlphaFold monomer V2.0 prediction for calpastatin (P27321) · a predicted model of the same protein · chain C against A, TM-score 0.59
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
- Every structure of UniProt Q64537
- Every structure of UniProt P27321
- Elsewhere: RCSB PDB 3BOW · PDBe 3BOW · UniProt Q07009 · UniProt Q64537 · UniProt P27321
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