MolNFT v1 · #42261 · protein
NMR structure of major S5A (196-306):K48 linked diubiquitin species
2KDE · 26S proteasome non-ATPase regulatory subunit 4: “NMR structure of major S5A (196-306):K48 linked diubiquitin species”. Solution nmr, 2 pockets (best druggability 0.57). MolNFT v1 #42261 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2KDE
- Type
- protein
- Length
- 263 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome non-ATPase regulatory subunit 4; Ubiquitin
- UniProt
- P55036, P62972
- Pockets
- 2 · best druggability 0.57
Structure
solution nmr · 2 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome non-ATPase regulatory subunit 4 | protein | 111 | 57% helix, 0% strand | P55036 |
| B, C | Ubiquitin | protein | 76 | 18% helix, 30% strand | P62972 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.57 | 0.74 | 51 | empty |
| 2 | 158 | 0.48 | 0.77 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 758 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2KDE · NMR structure of major S5a (196-306):K48 linked diubiquitin species · the same entry in another collection · chain A against A, TM-score 1.00
- P62972 · AlphaFold monomer V2.0 prediction for polyubiquitin (P62972) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P55036 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 4… · a predicted model of the same protein · chain A against A, TM-score 0.41
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 P55036
- Every structure of UniProt P62972
- Elsewhere: RCSB PDB 2KDE · PDBe 2KDE · UniProt P55036 · UniProt P62972
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.