MolNFT v1 · #16376 · protein
Calpain domain VI complexed with calpastatin inhibitory domain C (dic)
1NX1 · Calcium-dependent protease, small subunit: “Calpain domain VI complexed with calpastatin inhibitory domain C (dic)”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.77). MolNFT v1 #16376 on GenesisL1: 3D structure…
- PDB
- 1NX1
- Type
- protein
- Length
- 368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-dependent protease, small subunit; Calpastatin
- UniProt
- P04574, P49342
- Ligands
- CA
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 61% 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, D | Calpastatin | protein | 11 | 73% helix, 0% strand | P49342 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.77 | 0.98 | 27 | empty |
| 2 | 163 | 0.51 | 0.78 | 19 | empty |
| 3 | 145 | 0.50 | 0.78 | 22 | empty |
| 4 | 102 | 0.43 | 0.78 | 21 | empty |
| 5 | 99 | 0.41 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2280 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 650 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 632 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1NX1 · Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (DIC) · the same entry in another collection · chain A against A, 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 0.97
- P49342 · AlphaFold monomer V2.0 prediction for calpastatin (P49342) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 1NX1 · PDBe 1NX1 · UniProt P04574 · UniProt P49342
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