Research workbench
Structure of human SENP2 in complex with sumo-1
Analyse Structure of human SENP2 in complex with sumo-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TGZ
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 2; Ubiquitin-like protein SMT3C
- EC
- 3.4.22.-
- UniProt
- Q9HC62, P63165
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 2 (EC 3.4.22.-) | protein | 224 | 47% helix, 17% strand | Q9HC62 |
| B | Ubiquitin-like protein SMT3C | protein | 78 | 21% helix, 33% strand | P63165 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.61 | 0.79 | 30 | empty |
| 2 | 113 | 0.52 | 0.82 | 17 | empty |
| 3 | 150 | 0.42 | 0.74 | 25 | empty |
| 4 | 72 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1TGZ · Structure of human Senp2 in complex with SUMO-1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HC62 · AlphaFold monomer V2.0 prediction for sentrin-specific protease 2 (Q9HC62) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9HC62
- Every structure of UniProt P63165
- Elsewhere: RCSB PDB 1TGZ · PDBe 1TGZ · UniProt Q9HC62 · UniProt P63165
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