MolNFT v1 · #116652 · protein
Human ubiquitin in the P1 space group
5DK8 · Polyubiquitin-B: “Human ubiquitin in the P1 space group”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.30). MolNFT v1 #116652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DK8
- Type
- protein
- Length
- 151 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B
- UniProt
- P0CG47
- Ligands
- MG
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin-B | protein | 76 | 24% helix, 37% strand | P0CG47 |
| B | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
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 | 50 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DK8 · Human ubiquitin in the P1 space group · 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 5DK8 · PDBe 5DK8 · UniProt P0CG47
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