MolNFT v1 · #46360 · protein
Ubiquitin-conjugating enzyme E2-25 kda complexed with sumo-1- conjugating enzyme UBC9
2O25: “Ubiquitin-conjugating enzyme E2-25 kda complexed with sumo-1- conjugating enzyme UBC9”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #46360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2O25
- Type
- protein
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2-25 kda; Sumo-1-conjugating enzyme UBC9
- EC
- 6.3.2.19
- UniProt
- P61086, P63279
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2-25 kda (EC 6.3.2.19) | protein | 199 | 44% helix, 14% strand | P61086 |
| B | Ubiquitin-conjugating enzyme E2-25 kda (EC 6.3.2.19) | protein | 197 | 41% helix, 13% strand | P61086 |
| C | Sumo-1-conjugating enzyme UBC9 (EC 6.3.2.19) | protein | 157 | 34% helix, 20% strand | P63279 |
| D | Sumo-1-conjugating enzyme UBC9 (EC 6.3.2.19) | protein | 156 | 33% helix, 16% strand | P63279 |
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 | 1128 | 0.75 | 0.78 | 79 | empty |
| 2 | 67 | 0.44 | 0.82 | 15 | empty |
| 3 | 50 | 0.28 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 471 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 270 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2O25 · Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9 · 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 C against A, TM-score 0.99
- P61086 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 K (P61086) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P61086
- Every structure of UniProt P63279
- Elsewhere: RCSB PDB 2O25 · PDBe 2O25 · UniProt P61086 · UniProt P63279
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