MolNFT v1 · #139371 · protein
K11/48-branched teraubiquitin
5XDP · D-ubiquitin: “K11/48-branched teraubiquitin”. X-ray diffraction, 2 pockets (best druggability 0.34). MolNFT v1 #139371 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XDP
- Type
- protein
- Length
- 148 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ubiquitin; Ubiquitin-B
- UniProt
- P0CG47
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | D-ubiquitin | protein | 74 | 24% helix, 34% strand | — |
| A | Ubiquitin-B | protein | 74 | 26% helix, 35% strand | P0CG47 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.34 | 0.78 | 13 | empty |
| 2 | 55 | 0.27 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 326 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 69 d-amino, 1 modified (D-amino acid, nonstandard).
Compared structures
- 5XDP · K11/48-branched teraubiquitin · the same entry in another collection · chain B against B, 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 5XDP · PDBe 5XDP · UniProt P0CG47
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