MolNFT v1 · #144142 · protein
Crystal structure of human calpain-3 protease core in complex with leupeptin
6BKJ: “Crystal structure of human calpain-3 protease core in complex with leupeptin”. X-ray diffraction, 2 ligands (ACE, CA), 15 pockets (best druggability 0.81). MolNFT v1 #144142 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BKJ
- Type
- protein
- Length
- 1,237 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain-3; Leupeptin
- EC
- 3.4.22.54
- UniProt
- P20807
- Ligands
- ACE, CA
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-3 (EC 3.4.22.54) | protein | 307 | 30% helix, 23% strand | P20807 |
| B | Calpain-3 (EC 3.4.22.54) | protein | 307 | 29% helix, 23% strand | P20807 |
| C | Calpain-3 (EC 3.4.22.54) | protein | 304 | 30% helix, 23% strand | P20807 |
| D | Calpain-3 (EC 3.4.22.54) | protein | 307 | 29% helix, 23% strand | P20807 |
| F, G, H, I | Leupeptin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, F, G, C, H, D, I
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.81 | 0.83 | 93 | empty |
| 2 | 919 | 0.80 | 0.82 | 83 | ACE |
| 3 | 1194 | 0.77 | 0.79 | 95 | CA |
| 4 | 386 | 0.76 | 0.86 | 43 | empty |
| 5 | 383 | 0.74 | 0.85 | 42 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1134 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1127 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 306 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 299 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
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 6BKJ · PDBe 6BKJ · UniProt P20807
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