MolNFT v1 · #110597 · protein
UBC9 homodimer the missing link in poly-sumo chain formation
4Y1L · Sumo-conjugating enzyme UBC9: “UBC9 homodimer the missing link in poly-sumo chain formation”. X-ray diffraction, 1 pocket (best druggability 0.28). MolNFT v1 #110597 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y1L
- Type
- protein
- Length
- 424 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; Rwd domain-containing protein 3
- EC
- 6.3.2.-
- UniProt
- P63279, Q9Y3V2
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 158 | 35% helix, 20% strand | P63279 |
| B | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 157 | 36% helix, 20% strand | P63279 |
| C | Rwd domain-containing protein 3 | protein | 109 | 32% helix, 17% strand | Q9Y3V2 |
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 | 57 | 0.28 | 0.74 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4Y1L · Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation · the same entry in another collection · chain C against C, TM-score 1.00
- P63279 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P63279) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9Y3V2 · AlphaFold monomer V2.0 prediction for rwd domain-containing protein 3 (Q9Y3V2) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9Y3V2
- Elsewhere: RCSB PDB 4Y1L · PDBe 4Y1L · UniProt P63279 · UniProt Q9Y3V2
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