Research workbench
Structure of calpain domain 6 in complex with calpastatin dic
Analyse Structure of calpain domain 6 in complex with calpastatin dic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NX0
- Type
- protein
- Length
- 374 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-dependent protease, small subunit; Calpastatin; Small molecule inhibitor
- UniProt
- P04574, P49342
- Ligands
- CA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Calcium-dependent protease, small subunit | protein | 173 | 61% helix, 5% strand | P04574 |
| C | Calpastatin | protein | 12 | 50% helix, 0% strand | P49342 |
| D | Calpastatin | protein | 11 | 73% helix, 0% strand | P49342 |
| E | Small molecule inhibitor | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
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 | 285 | 0.68 | 0.83 | 55 | empty |
| 2 | 139 | 0.50 | 0.79 | 21 | empty |
| 3 | 134 | 0.48 | 0.78 | 20 | empty |
| 4 | 97 | 0.44 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2235 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 581 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 289 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1NX0 · Structure of Calpain Domain 6 in Complex with Calpastatin DIC · the same entry in another collection · chain E against E, TM-score 1.00
- P04574 · AlphaFold monomer V2.0 prediction for calpain small subunit 1 (P04574) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P49342 · AlphaFold monomer V2.0 prediction for calpastatin (P49342) · a predicted model of the same protein · chain D against A, TM-score 0.58
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 P04574
- Every structure of UniProt P49342
- Elsewhere: RCSB PDB 1NX0 · PDBe 1NX0 · UniProt P04574 · UniProt P49342
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