MolNFT v1 · #140805 · protein
The structure of the complex between RPN13 and K48-diub
5YMY · Ubiquitin: “The structure of the complex between RPN13 and K48-diub”. Solution nmr, 4 pockets (best druggability 0.55). MolNFT v1 #140805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YMY
- Type
- protein
- Length
- 266 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Proteasomal ubiquitin receptor ADRM1
- UniProt
- P0CG47, Q16186
- Pockets
- 4 · best druggability 0.55
Structure
solution nmr · 3 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
| B | Ubiquitin | protein | 76 | 24% helix, 32% strand | P0CG47 |
| C | Proteasomal ubiquitin receptor ADRM1 | protein | 114 | 11% helix, 46% strand | Q16186 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.55 | 0.82 | 25 | empty |
| 2 | 160 | 0.47 | 0.76 | 22 | empty |
| 3 | 66 | 0.31 | 0.74 | 14 | empty |
| 4 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 645 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 550 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5YMY · The structure of the complex between Rpn13 and K48-diUb · the same entry in another collection · chain A against A, TM-score 1.00
- Q16186 · AlphaFold monomer V2.0 prediction for proteasomal ubiquitin receptor ADRM1 (Q16186) · a predicted model of the same protein · chain C against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 5YMY · PDBe 5YMY · UniProt P0CG47 · UniProt Q16186
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