Research workbench
Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit
Analyse Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EMZ
- Type
- protein
- Length
- 448 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B
- UniProt
- P0CG47
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Polyubiquitin-B | protein | 76 | 20% helix, 34% strand | P0CG47 |
| B | Polyubiquitin-B | protein | 74 | 24% helix, 35% strand | P0CG47 |
| D, F | Polyubiquitin-B | protein | 73 | 21% helix, 36% strand | P0CG47 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.80 | 0.84 | 65 | empty |
| 2 | 310 | 0.61 | 0.78 | 46 | empty |
| 3 | 69 | 0.32 | 0.75 | 18 | empty |
| 4 | 59 | 0.28 | 0.74 | 22 | empty |
Interfaces
11 interfaces between chains.
- A–B · 749 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 690 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 662 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 528 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 372 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 5EMZ · Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit · 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 5EMZ · PDBe 5EMZ · UniProt P0CG47
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