Research workbench
Structure of LYS33-linked diub
Analyse Structure of LYS33-linked diub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AF4
- Type
- protein
- Length
- 599 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- Q96C32
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Ubiquitin | protein | 76 | 24% helix, 33% strand | Q96C32 |
| B, D | Ubiquitin | protein | 75 | 24% helix, 33% strand | Q96C32 |
| F, H | Ubiquitin | protein | 74 | 24% helix, 34% strand | Q96C32 |
| G | Ubiquitin | protein | 73 | 21% helix, 34% strand | Q96C32 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, E, F, D, G
- GOL · Glycerol · additive · 9 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.78 | 0.80 | 113 | GOL, SO4 |
| 2 | 121 | 0.37 | 0.73 | 25 | empty |
| 3 | 54 | 0.27 | 0.74 | 14 | empty |
| 4 | 54 | 0.26 | 0.74 | 13 | empty |
Interfaces
14 interfaces between chains.
- A–B · 878 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 876 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 768 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 447 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 5AF4 · Structure of Lys33-linked diUb · 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 Q96C32
- Elsewhere: RCSB PDB 5AF4 · PDBe 5AF4 · UniProt Q96C32
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