Research workbench
Calcium-dependent complex between M-calpain and calpastatin
Analyse Calcium-dependent complex between M-calpain and calpastatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DF0
- Type
- protein
- Length
- 906 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
- 16 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-2 catalytic subunit (EC 3.4.22.53) | protein | 676 | 28% helix, 22% strand | Q07009 |
| B | Calpain small subunit 1 | protein | 174 | 61% helix, 6% strand | Q64537 |
| C | Calpastatin | protein | 56 | 34% helix, 4% 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.79 | 0.83 | 98 | empty |
| 2 | 257 | 0.71 | 0.86 | 47 | empty |
| 3 | 293 | 0.62 | 0.80 | 40 | empty |
| 4 | 229 | 0.61 | 0.81 | 32 | empty |
| 5 | 305 | 0.59 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2422 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2235 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 606 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3DF0 · Calcium-dependent complex between m-calpain and 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 0.80
- P27321 · AlphaFold monomer V2.0 prediction for calpastatin (P27321) · a predicted model of the same protein · chain C against A, TM-score 0.60
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 3DF0 · PDBe 3DF0 · UniProt Q07009 · UniProt Q64537 · UniProt P27321
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