Research workbench
The crystal structure of the SLD2:UBC9 complex
Analyse The crystal structure of the SLD2:UBC9 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A4S
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; NFATC2-interacting protein
- EC
- 6.3.2.-
- UniProt
- P63279, O09130
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 155 | 34% helix, 19% strand | P63279 |
| B | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 155 | 34% helix, 19% strand | P63279 |
| C | NFATC2-interacting protein | protein | 74 | 18% helix, 31% strand | O09130 |
| D | NFATC2-interacting protein | protein | 62 | 13% helix, 34% strand | O09130 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.70 | 0.82 | 36 | empty |
| 2 | 171 | 0.46 | 0.75 | 35 | empty |
| 3 | 114 | 0.37 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 578 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A4S · The crystal structure of the SLD2:Ubc9 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P63279 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P63279) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O09130 · AlphaFold monomer V2.0 prediction for NFATC2-interacting protein (O09130) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P63279
- Every structure of UniProt O09130
- Elsewhere: RCSB PDB 3A4S · PDBe 3A4S · UniProt P63279 · UniProt O09130
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