Research workbench
Crystal structure of K11-linked diubiquitin
Analyse Crystal structure of K11-linked diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XEW
- Type
- protein
- Length
- 908 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P62988
- Ligands
- CL
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H, I, J, K | Ubiquitin | protein | 76 | 24% helix, 34% strand | P62988 |
| C, L | Ubiquitin | protein | 74 | 24% helix, 34% strand | P62988 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, C, D, I, L
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, G, B, F, C, D, E, H, I, J, K, L
- FLC · Citrate anion · additive · 2 copies · chains A, B, F, G, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.74 | 0.78 | 77 | FLC |
| 2 | 161 | 0.49 | 0.78 | 23 | CL |
| 3 | 192 | 0.49 | 0.76 | 29 | EDO |
| 4 | 164 | 0.49 | 0.78 | 26 | empty |
| 5 | 166 | 0.48 | 0.77 | 26 | EDO, CL |
Interfaces
23 interfaces between chains.
- J–K · 887 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 829 Ų buried · 6 hydrogen bonds · protein-protein
- I–L · 826 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 825 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 824 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 isopeptide (isopeptide).
Compared structures
- 2XEW · Crystal structure of K11-linked diubiquitin · 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 P62988
- Elsewhere: RCSB PDB 2XEW · PDBe 2XEW · UniProt P62988
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