MolNFT v1 · #143920 · protein
Crystal structure of human calpain-3 protease core mutant-C129S
6BDT: “Crystal structure of human calpain-3 protease core mutant-C129S”. X-ray diffraction, 2 ligands (CA, CL), 16 pockets (best druggability 0.82). MolNFT v1 #143920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BDT
- Type
- protein
- Length
- 1,258 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
- CA, CL
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-3 (EC 3.4.22.54) | protein | 307 | 30% helix, 22% strand | P20807 |
| B | Calpain-3 (EC 3.4.22.54) | protein | 318 | 29% helix, 22% strand | P20807 |
| C | Calpain-3 (EC 3.4.22.54) | protein | 318 | 29% helix, 23% strand | P20807 |
| D | Calpain-3 (EC 3.4.22.54) | protein | 315 | 30% helix, 23% strand | P20807 |
Ligands and binding sites
- 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 | 998 | 0.82 | 0.84 | 97 | empty |
| 2 | 934 | 0.79 | 0.82 | 82 | empty |
| 3 | 382 | 0.74 | 0.85 | 35 | empty |
| 4 | 422 | 0.71 | 0.82 | 39 | empty |
| 5 | 279 | 0.55 | 0.76 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1442 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1285 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 725 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 109 Ų buried · 1 hydrogen bond · 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 6BDT · PDBe 6BDT · UniProt P20807
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