Research workbench
Crystal structure of cyld usp domain (C596S E674Q) in complex with MET1-linked diubiquitin
Analyse Crystal structure of cyld usp domain (C596S E674Q) in complex with MET1-linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WXF
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; Ubiquitin
- UniProt
- E7FEV5, P0CG48
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 299 | 32% helix, 25% strand | E7FEV5 |
| B, D | Ubiquitin | protein | 148 | 22% helix, 34% strand | P0CG48 |
| C | Uncharacterized protein | protein | 299 | 32% helix, 25% strand | E7FEV5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.76 | 0.79 | 73 | empty |
| 2 | 483 | 0.72 | 0.81 | 45 | empty |
| 3 | 311 | 0.64 | 0.80 | 37 | empty |
| 4 | 319 | 0.63 | 0.80 | 41 | empty |
| 5 | 215 | 0.56 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1950 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1909 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 500 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 270 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WXF · Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-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 E7FEV5
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 3WXF · PDBe 3WXF · UniProt E7FEV5 · UniProt P0CG48
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