MolNFT v1 · #109035 · protein
Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound
4WQ2 · Calpain small subunit 1: “Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound”. X-ray diffraction, 2 ligands (3SU, CA), 7 pockets (best druggability 0.76). MolNFT v1 #109035 on GenesisL1: 3D structure…
- PDB
- 4WQ2
- 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
- 7 · best druggability 0.76
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 · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.76 | 0.96 | 24 | empty |
| 2 | 79 | 0.49 | 0.83 | 11 | 3SU |
| 3 | 149 | 0.49 | 0.78 | 20 | EDO |
| 4 | 81 | 0.48 | 0.81 | 15 | 3SU |
| 5 | 144 | 0.46 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2311 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4WQ2 · Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound · 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 4WQ2 · PDBe 4WQ2 · UniProt P04632
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