MolNFT v1 · #12987 · protein
Crystal structure of calcium-bound protease core of calpain I
1KXR · Thiol protease domains I and II: “Crystal structure of calcium-bound protease core of calpain I”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.43). MolNFT v1 #12987 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KXR
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol protease domains I and II
- EC
- 3.4.22.17
- UniProt
- P97571
- Ligands
- CA
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiol protease domains I and II (EC 3.4.22.17) | protein | 320 | 32% helix, 23% strand | P97571 |
| B | Thiol protease domains I and II (EC 3.4.22.17) | protein | 321 | 32% helix, 23% strand | P97571 |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.43 | 0.77 | 25 | empty |
| 2 | 89 | 0.40 | 0.78 | 21 | empty |
| 3 | 51 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 356 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1KXR · Crystal Structure of Calcium-Bound Protease Core of Calpain I · the same entry in another collection · chain A against A, TM-score 1.00
- P97571 · AlphaFold monomer V2.0 prediction for calpain-1 catalytic subunit (P97571) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P97571
- Elsewhere: RCSB PDB 1KXR · PDBe 1KXR · UniProt P97571
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