Research workbench
Human calpain PEF(S) with (2Z,2Z')-2,2'-DISULFANEDIYLBIS(3-(6- bromoindol-3-YL)ACRYLIC acid) bound
Analyse Human calpain PEF(S) with (2Z,2Z')-2,2'-DISULFANEDIYLBIS(3-(6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WQ3
- 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
- 3SU, CA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Calpain small subunit 1 | protein | 173 | 62% helix, 6% strand | P04632 |
Ligands and binding sites
- 3SU · (2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic acid · ligand · 4 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 | 307 | 0.57 | 0.77 | 46 | empty |
| 2 | 82 | 0.53 | 0.84 | 14 | 3SU |
| 3 | 68 | 0.44 | 0.81 | 12 | 3SU |
| 4 | 121 | 0.44 | 0.77 | 17 | empty |
| 5 | 125 | 0.44 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2258 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4WQ3 · Human calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-bromoindol-3-yl)acrylic… · 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 B 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 4WQ3 · PDBe 4WQ3 · UniProt P04632
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