Research workbench
Solution structure of the RPN1 T1 site with K48-linked diubiquitin in the contracted binding mode
Analyse Solution structure of the RPN1 T1 site with K48-linked diubiquitin in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2N3W
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit RPN1; Ubiquitin-60S ribosomal protein L40
- UniProt
- P38764, P62987
- Pockets
- 6 · best druggability 0.67
Structure
solution nmr · 2 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN1 | protein | 131 | 59% helix, 0% strand | P38764 |
| B, C | Ubiquitin-60S ribosomal protein L40 | protein | 76 | 14% helix, 30% strand | P62987 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.67 | 0.94 | 17 | empty |
| 2 | 387 | 0.66 | 0.79 | 49 | empty |
| 3 | 191 | 0.55 | 0.80 | 29 | empty |
| 4 | 174 | 0.49 | 0.77 | 33 | empty |
| 5 | 94 | 0.45 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 730 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2N3W · Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted… · the same entry in another collection · chain A against A, TM-score 1.00
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P38764 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN1 (P38764) · a predicted model of the same protein · chain A against A, TM-score 0.70
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 P38764
- Every structure of UniProt P62987
- Elsewhere: RCSB PDB 2N3W · PDBe 2N3W · UniProt P38764 · UniProt P62987
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