Research workbench
Crystal structure of calpain-3 penta-ef-hand domain
Analyse Crystal structure of calpain-3 penta-ef-hand domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OKH
- Type
- protein
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain-3
- EC
- 3.4.22.54
- UniProt
- P20807
- Ligands
- PEU, CA
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-3 (EC 3.4.22.54) | protein | 171 | 60% helix, 7% strand | P20807 |
| B | Calpain-3 (EC 3.4.22.54) | protein | 170 | 62% helix, 7% strand | P20807 |
| C | Calpain-3 (EC 3.4.22.54) | protein | 147 | 63% helix, 5% strand | P20807 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.57 | 0.78 | 27 | empty |
| 2 | 324 | 0.57 | 0.76 | 29 | empty |
| 3 | 336 | 0.54 | 0.74 | 30 | empty |
| 4 | 119 | 0.46 | 0.78 | 13 | empty |
| 5 | 133 | 0.40 | 0.74 | 19 | PEU |
Interfaces
2 interfaces between chains.
- A–B · 1874 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P20807
- Elsewhere: RCSB PDB 4OKH · PDBe 4OKH · UniProt P20807
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