Research workbench
Human calpain PEF(S) with (2Z,2Z')-2,2'-DISULFANEDIYLBIS(3-(6- iodoindol-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
- 5D69
- 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
- 57T, CA, SO4
- Pockets
- 8 · best druggability 0.75
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
- 57T · (2E,2'Z)-2,2'-disulfanediylbis[3-(4-iodophenyl)prop-2-enoic acid] · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.75 | 0.96 | 23 | empty |
| 2 | 63 | 0.50 | 0.85 | 12 | empty |
| 3 | 143 | 0.47 | 0.78 | 28 | CA |
| 4 | 166 | 0.47 | 0.76 | 28 | empty |
| 5 | 118 | 0.45 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2314 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 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 5D69 · PDBe 5D69 · UniProt P04632
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