Research workbench
Solution structure of sumo dimer in complex with SIM2-3 from RNF4
Analyse Solution structure of sumo dimer in complex with SIM2-3 from RNF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MP2
- Type
- protein
- Length
- 197 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small ubiquitin-related modifier 3; E3 ubiquitin-protein ligase RNF4
- UniProt
- P55854, Q9QZS2
- Pockets
- 1 · best druggability 0.41
Structure
solution nmr · 3 distinct chains · 14% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small ubiquitin-related modifier 3 | protein | 82 | 16% helix, 26% strand | P55854 |
| B | Small ubiquitin-related modifier 3 | protein | 90 | 17% helix, 21% strand | P55854 |
| C | E3 ubiquitin-protein ligase RNF4 | protein | 25 | 0% helix, 0% strand | Q9QZS2 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.41 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 728 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 606 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2MP2 · Solution structure of SUMO dimer in complex with SIM2-3 from RNF4 · the same entry in another collection · chain A against A, TM-score 1.00
- P55854 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 3 (P55854) · a predicted model of the same protein · chain A against A, TM-score 0.78
- Q9QZS2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF4 (Q9QZS2) · a predicted model of the same protein · chain C against A, TM-score 0.18
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 P55854
- Every structure of UniProt Q9QZS2
- Elsewhere: RCSB PDB 2MP2 · PDBe 2MP2 · UniProt P55854 · UniProt Q9QZS2
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