MolNFT v1 · #40618 · protein
SENP1 (mutant) full length SUMO1
2IY1 · Sentrin-specific protease 1: “SENP1 (mutant) full length SUMO1”. X-ray diffraction, 10 pockets (best druggability 0.64). MolNFT v1 #40618 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IY1
- Type
- protein
- Length
- 618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 1; Small ubiquitin-related modifier 1
- EC
- 3.4.22.-
- UniProt
- Q9P0U3, P63165
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Sentrin-specific protease 1 (EC 3.4.22.-) | protein | 226 | 42% helix, 16% strand | Q9P0U3 |
| B, D | Small ubiquitin-related modifier 1 | protein | 83 | 22% helix, 33% strand | P63165 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.64 | 0.80 | 35 | empty |
| 2 | 271 | 0.64 | 0.81 | 30 | empty |
| 3 | 158 | 0.61 | 0.84 | 23 | empty |
| 4 | 154 | 0.59 | 0.84 | 23 | empty |
| 5 | 52 | 0.41 | 0.82 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1262 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1260 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2IY1 · SENP1 (mutant) full length SUMO1 · 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
- 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 0.88
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
- Elsewhere: RCSB PDB 2IY1 · PDBe 2IY1 · UniProt Q9P0U3 · UniProt P63165
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