Research workbench
The structural basis of differential inhibition of human calpain by indole and phenyl alpha-mercaptoacrylic acids. the complex with (Z)- 3-(4-chlorophenyl)-2-mercaptoacrylic acid
Analyse The structural basis of differential inhibition of human calpain by indole and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHK
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain small subunit 1
- UniProt
- P04632
- Ligands
- 2UB, CA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Calpain small subunit 1 | protein | 173 | 63% helix, 6% strand | P04632 |
Ligands and binding sites
- 2UB · (Z)-3-(4-chlorophenyl)-2-mercaptoacrylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.76 | 0.97 | 23 | empty |
| 2 | 156 | 0.50 | 0.79 | 28 | empty |
| 3 | 141 | 0.47 | 0.78 | 25 | empty |
| 4 | 126 | 0.45 | 0.77 | 18 | empty |
| 5 | 126 | 0.42 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2258 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4PHK · The Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P04632 · AlphaFold monomer V2.0 prediction for calpain small subunit 1 (P04632) · a predicted model of the same protein · chain A 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 P04632
- Elsewhere: RCSB PDB 4PHK · PDBe 4PHK · UniProt P04632
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