Research workbench
SENP1 (mutant) SUMO1 rangap
Analyse SENP1 (mutant) SUMO1 rangap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IY0
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 1; Small ubiquitin-related modifier 1; Ran GTPase-activating…
- EC
- 3.4.22.-
- UniProt
- Q9P0U3, P63165, P46060
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 1 (EC 3.4.22.-) | protein | 226 | 42% helix, 17% strand | Q9P0U3 |
| B | Small ubiquitin-related modifier 1 | protein | 76 | 18% helix, 32% strand | P63165 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 63% helix, 0% strand | P46060 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.63 | 0.81 | 29 | empty |
| 2 | 185 | 0.57 | 0.81 | 23 | empty |
| 3 | 220 | 0.50 | 0.76 | 26 | empty |
| 4 | 124 | 0.45 | 0.78 | 18 | empty |
| 5 | 96 | 0.44 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1097 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 416 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2IY0 · SENP1 (mutant) SUMO1 RanGAP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P0U3 · AlphaFold monomer V2.0 prediction for sentrin-specific protease 1 (Q9P0U3) · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 0.98
- 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 Q9P0U3
- Every structure of UniProt P63165
- Every structure of UniProt P46060
- Elsewhere: RCSB PDB 2IY0 · PDBe 2IY0 · UniProt Q9P0U3 · UniProt P63165 · UniProt P46060
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