MolNFT v1 · #40630 · protein
SENP1 covalent complex with sumo-2
2IYD · Sentrin-specific protease 1: “SENP1 covalent complex with sumo-2”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #40630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IYD
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 1; Small ubiquitin-related modifier 2
- EC
- 3.4.22.-
- UniProt
- Q9P0U3, P61956
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 1 (EC 3.4.22.-) | protein | 226 | 41% helix, 17% strand | Q9P0U3 |
| B | Small ubiquitin-related modifier 2 | protein | 79 | 15% helix, 39% strand | P61956 |
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 | 253 | 0.63 | 0.81 | 27 | empty |
| 2 | 208 | 0.58 | 0.80 | 26 | empty |
| 3 | 51 | 0.40 | 0.82 | 14 | empty |
| 4 | 85 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2IYD · SENP1 covalent complex with SUMO-2 · 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
- P61956 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 2 (P61956) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P61956
- Elsewhere: RCSB PDB 2IYD · PDBe 2IYD · UniProt Q9P0U3 · UniProt P61956
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