Research workbench
Catalytic domain of SST2 F403W mutant bound to ubiquitin
Analyse Catalytic domain of SST2 F403W mutant bound to ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFT
- Type
- protein
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amsh-like protease SST2; Polyubiquitin-B
- EC
- 3.4.19.-
- UniProt
- Q9P371, P0CG47
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 185 | 26% helix, 35% strand | Q9P371 |
| B | Polyubiquitin-B | protein | 78 | 19% helix, 38% strand | P0CG47 |
| C | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 183 | 27% helix, 34% strand | Q9P371 |
| D | Polyubiquitin-B | protein | 77 | 19% helix, 39% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.57 | 0.82 | 20 | empty |
| 2 | 131 | 0.44 | 0.77 | 21 | empty |
| 3 | 144 | 0.44 | 0.76 | 29 | empty |
| 4 | 104 | 0.41 | 0.77 | 13 | empty |
| 5 | 95 | 0.40 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1237 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1218 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 347 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P0CG47
- Elsewhere: RCSB PDB 4ZFT · PDBe 4ZFT · UniProt Q9P371 · UniProt P0CG47
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