Research workbench
Structure of a sumo-binding-motif mimic bound to SMT3P- UBC9P: conservation of a noncovalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a sumo pathway
Analyse Structure of a sumo-binding-motif mimic bound to SMT3P- UBC9P: conservation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EKE
- Type
- protein
- Length
- 487 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; Ubiquitin-like protein SMT3
- EC
- 6.3.2.19
- UniProt
- P50623, Q12306
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sumo-conjugating enzyme UBC9 (EC 6.3.2.19) | protein | 154 | 35% helix, 19% strand | P50623 |
| C | Ubiquitin-like protein SMT3 | protein | 91 | 15% helix, 31% strand | Q12306 |
| D | Ubiquitin-like protein SMT3 | protein | 88 | 16% helix, 32% strand | Q12306 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.69 | 0.77 | 70 | empty |
| 2 | 86 | 0.41 | 0.78 | 19 | empty |
| 3 | 78 | 0.35 | 0.75 | 14 | empty |
| 4 | 78 | 0.33 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 577 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 572 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2EKE · Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a… · the same entry in another collection · chain A against A, TM-score 1.00
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P50623
- Every structure of UniProt Q12306
- Elsewhere: RCSB PDB 2EKE · PDBe 2EKE · UniProt P50623 · UniProt Q12306
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.