Research workbench
Solution structure of the RPN1 T1 site engaging two monoubiquitin molecules
Analyse Solution structure of the RPN1 T1 site engaging two monoubiquitin molecules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2N3U
- 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 0.64
Structure
solution nmr · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN1 | protein | 131 | 61% helix, 0% strand | P38764 |
| B, C | Ubiquitin-60S ribosomal protein L40 | protein | 76 | 18% helix, 29% strand | P62987 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.64 | 0.83 | 40 | empty |
| 2 | 68 | 0.57 | 0.89 | 20 | empty |
| 3 | 51 | 0.39 | 0.81 | 11 | empty |
| 4 | 50 | 0.38 | 0.81 | 15 | empty |
| 5 | 74 | 0.34 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 889 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 226 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2N3U · Solution structure of the Rpn1 T1 site engaging two monoubiquitin molecules · 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 0.92
- 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 0.74
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 2N3U · PDBe 2N3U · UniProt P38764 · UniProt P62987
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