Research workbench
Crystal structure of human SENP2 in complex with RANGAP1-sumo-1
Analyse Crystal structure of human SENP2 in complex with RANGAP1-sumo-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IO2
- Type
- protein
- Length
- 456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 2; Small ubiquitin-related modifier 1; Ran GTPase-activating…
- EC
- 3.4.22.-
- UniProt
- Q9HC62, P63165, P46060
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 2 (EC 3.4.22.-) | protein | 225 | 39% helix, 15% strand | Q9HC62 |
| B | Small ubiquitin-related modifier 1 | protein | 75 | 19% helix, 20% strand | P63165 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 69% helix, 0% strand | P46060 |
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 | 299 | 0.64 | 0.80 | 29 | empty |
| 2 | 110 | 0.54 | 0.83 | 24 | empty |
| 3 | 184 | 0.49 | 0.77 | 21 | empty |
| 4 | 70 | 0.33 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1057 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 616 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 148 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2IO2 · Crystal structure of human Senp2 in complex with RanGAP1-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 0.90
- P46060 · AlphaFold monomer V2.0 prediction for ran GTPase-activating protein 1 (P46060) · a predicted model of the same protein · chain C against A, TM-score 0.65
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
- Every structure of UniProt P46060
- Elsewhere: RCSB PDB 2IO2 · PDBe 2IO2 · UniProt Q9HC62 · UniProt P63165 · UniProt P46060
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