MolNFT v1 · #144100 · protein
Crystal structure of human calpain-3 protease core in complex with E- 64
6BJD: “Crystal structure of human calpain-3 protease core in complex with E- 64”. X-ray diffraction, 4 ligands (E64, SOR, CA), 16 pockets (best druggability 0.81). MolNFT v1 #144100 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BJD
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain-3
- EC
- 3.4.22.54
- UniProt
- P20807
- Ligands
- E64, SOR, CA, CL
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-3 (EC 3.4.22.54) | protein | 313 | 30% helix, 23% strand | P20807 |
| B | Calpain-3 (EC 3.4.22.54) | protein | 305 | 31% helix, 23% strand | P20807 |
| C | Calpain-3 (EC 3.4.22.54) | protein | 306 | 31% helix, 23% strand | P20807 |
| D | Calpain-3 (EC 3.4.22.54) | protein | 305 | 31% helix, 23% strand | P20807 |
Ligands and binding sites
- E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · 4 copies · chains A, C, B, D
- SOR · sorbitol · ligand · chains B
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.81 | 0.85 | 72 | empty |
| 2 | 250 | 0.74 | 0.89 | 32 | empty |
| 3 | 532 | 0.69 | 0.79 | 57 | empty |
| 4 | 225 | 0.68 | 0.85 | 29 | empty |
| 5 | 235 | 0.55 | 0.78 | 21 | E64 |
Interfaces
3 interfaces between chains.
- B–C · 1407 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 745 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 6BJD · PDBe 6BJD · UniProt P20807
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