Research workbench
HRPN13:HRPN2:K48-diubiquitin
Analyse HRPN13:HRPN2:K48-diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYI
- Type
- protein
- Length
- 280 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Proteasomal ubiquitin receptor ADRM1; 26S proteasome non-ATPase regulatory…
- UniProt
- P0CG47, Q16186, Q99460
- Pockets
- 3 · best druggability 0.45
Structure
solution nmr · 4 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubiquitin | protein | 77 | 19% helix, 29% strand | P0CG47 |
| D | Ubiquitin | protein | 76 | 20% helix, 32% strand | P0CG47 |
| A | Proteasomal ubiquitin receptor ADRM1 | protein | 113 | 11% helix, 53% strand | Q16186 |
| B | 26S proteasome non-ATPase regulatory subunit 1 | protein | 14 | 0% helix, 14% strand | Q99460 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.45 | 0.80 | 24 | empty |
| 2 | 101 | 0.35 | 0.73 | 16 | empty |
| 3 | 67 | 0.29 | 0.73 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 822 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 544 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 265 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 139 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6UYI · hRpn13:hRpn2:K48-diubiquitin · the same entry in another collection · chain C against C, TM-score 1.00
- Q16186 · AlphaFold monomer V2.0 prediction for proteasomal ubiquitin receptor ADRM1 (Q16186) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q99460 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 1… · a predicted model of the same protein · chain B against A, TM-score 0.25
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 P0CG47
- Every structure of UniProt Q16186
- Every structure of UniProt Q99460
- Elsewhere: RCSB PDB 6UYI · PDBe 6UYI · UniProt P0CG47 · UniProt Q16186 · UniProt Q99460
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