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Crystal structure of S. pombe amsh-like protease SST2 catalytic domain from P212121 space group
Analyse Crystal structure of S. pombe amsh-like protease SST2 catalytic domain from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MSJ
- Type
- protein
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amsh-like protease SST2
- EC
- 3.4.19.-
- UniProt
- Q9P371
- Ligands
- GLY, ZN, PO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 190 | 25% helix, 32% strand | Q9P371 |
| B | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 188 | 24% helix, 31% strand | Q9P371 |
| C | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 187 | 25% helix, 35% strand | Q9P371 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.75 | 0.81 | 65 | EDO |
| 2 | 233 | 0.64 | 0.82 | 35 | empty |
| 3 | 169 | 0.51 | 0.78 | 25 | empty |
| 4 | 114 | 0.41 | 0.76 | 25 | EDO |
| 5 | 90 | 0.39 | 0.76 | 21 | EDO |
Interfaces
2 interfaces between chains.
- B–C · 959 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4MSJ · Crystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121 space… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P371 · AlphaFold monomer V2.0 prediction for amsh-like protease SST2 (Q9P371) · a predicted model of the same protein · chain C 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
- Elsewhere: RCSB PDB 4MSJ · PDBe 4MSJ · UniProt Q9P371
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