MolNFT v1 · #123174 · protein
LYS27-linked triubiquitin
5JBV: “LYS27-linked triubiquitin”. X-ray diffraction, 1 ligand (NO3), 1 pocket (best druggability 0.29). MolNFT v1 #123174 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JBV
- Type
- protein
- Length
- 147 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; D-ubiquitin
- UniProt
- P0CG47
- Ligands
- NO3
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 22% helix, 37% strand | P0CG47 |
| B | D-ubiquitin | protein | 71 | 27% helix, 34% strand | — |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.29 | 0.75 | 16 | NO3 |
Interfaces
1 interface between chains.
- A–B · 379 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 d-amino, 1 modified (D-amino acid, nonstandard).
Compared structures
- 5JBV · Lys27-linked triubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 5JBV · PDBe 5JBV · UniProt P0CG47
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