Research workbench
NMR structure of minor S5a (196-306):K48 linked diubiquitin species
Analyse NMR structure of minor S5a (196-306):K48 linked diubiquitin species in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KDF
- Type
- protein
- Length
- 263 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Source
- Homo sapiens
- Molecule
- 26S proteasome non-ATPase regulatory subunit 4; Ubiquitin
- UniProt
- P55036, P62988
- Pockets
- 2 · best druggability 0.35
Structure
solution nmr · resolution NOT · 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 | 56% helix, 0% strand | P55036 |
| B, C | Ubiquitin | protein | 76 | 18% helix, 30% strand | P62988 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.35 | 0.78 | 11 | empty |
| 2 | 71 | 0.31 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 519 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 504 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 106 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2KDF · NMR structure of minor S5A (196-306):K48 linked diubiquitin species · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.35
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 P62988
- Elsewhere: RCSB PDB 2KDF · PDBe 2KDF · UniProt P55036 · UniProt P62988
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