MolNFT v1 · #100272 · protein
Crystal structure of schizosaccharomyces pombe amsh-like protease SST2 E286A mutant bound to ubiquitin
4MSM: “Crystal structure of schizosaccharomyces pombe amsh-like protease SST2 E286A mutant bound to ubiquitin”. X-ray diffraction, 2 ligands (ZN, PO4), 3 pockets (best druggability 0.52). MolNFT v1 #100272 on GenesisL1: 3D structure…
- PDB
- 4MSM
- Type
- protein
- Length
- 524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amsh-like protease SST2; Ubiquitin
- EC
- 3.4.19.-
- UniProt
- Q9P371, P0CG48
- Ligands
- ZN, PO4
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 186 | 26% helix, 34% strand | Q9P371 |
| B, D | Ubiquitin | protein | 76 | 24% helix, 36% strand | P0CG48 |
| C | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 186 | 26% helix, 34% strand | Q9P371 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.52 | 0.77 | 19 | empty |
| 2 | 189 | 0.48 | 0.76 | 29 | EDO |
| 3 | 207 | 0.47 | 0.75 | 41 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1252 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1225 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4MSM · Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9P371 · AlphaFold monomer V2.0 prediction for amsh-like protease SST2 (Q9P371) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9P371
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4MSM · PDBe 4MSM · UniProt Q9P371 · UniProt P0CG48
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