Research workbench
Crystal structure of human SENP2 in complex with RANGAP1-sumo-2
Analyse Crystal structure of human SENP2 in complex with RANGAP1-sumo-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IO3
- Type
- protein
- Length
- 454 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 2; Small ubiquitin-related modifier 2; Ran GTPase-activating…
- EC
- 3.4.22.-
- UniProt
- Q9HC62, P61956, P46060
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 2 (EC 3.4.22.-) | protein | 224 | 36% helix, 15% strand | Q9HC62 |
| B | Small ubiquitin-related modifier 2 | protein | 74 | 12% helix, 24% strand | P61956 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 63% helix, 0% strand | P46060 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.69 | 0.80 | 40 | empty |
| 2 | 229 | 0.60 | 0.80 | 24 | empty |
| 3 | 59 | 0.55 | 0.88 | 16 | empty |
| 4 | 100 | 0.49 | 0.81 | 19 | empty |
| 5 | 73 | 0.46 | 0.82 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1056 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 157 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2IO3 · Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2 · the same entry in another collection · chain B against B, 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
- 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 0.88
- 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 P61956
- Every structure of UniProt P46060
- Elsewhere: RCSB PDB 2IO3 · PDBe 2IO3 · UniProt Q9HC62 · UniProt P61956 · UniProt P46060
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