Research workbench
Crystal structure of K29 linked di-ubiquitin
Analyse Crystal structure of K29 linked di-ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S22
- Type
- protein
- Length
- 298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- E1B9K1
- Ligands
- IOD
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin | protein | 73 | 25% helix, 36% strand | E1B9K1 |
| B, D | Ubiquitin | protein | 76 | 24% helix, 33% strand | E1B9K1 |
Ligands and binding sites
- IOD · Iodide ion · ion · 6 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · chains B
- GOL · Glycerol · additive · chains D
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 | 172 | 0.43 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 266 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 233 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 196 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 4S22 · Crystal structure of K29 linked di-Ubiquitin · 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 E1B9K1
- Elsewhere: RCSB PDB 4S22 · PDBe 4S22 · UniProt E1B9K1
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