Research workbench
Crystal structure of cyld usp domain (C596A) in complex with LYS63- linked diubiquitin
Analyse Crystal structure of cyld usp domain (C596A) in complex with LYS63- linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WXG
- Type
- protein
- Length
- 896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; Ubiquitin
- UniProt
- E7FEV5, P0CG50
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uncharacterized protein | protein | 300 | 32% helix, 25% strand | E7FEV5 |
| B, E | Ubiquitin | protein | 76 | 16% helix, 32% strand | P0CG50 |
| C, F | Ubiquitin | protein | 72 | 17% helix, 35% strand | P0CG50 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.76 | 0.80 | 54 | empty |
| 2 | 318 | 0.61 | 0.79 | 35 | empty |
| 3 | 348 | 0.61 | 0.78 | 36 | empty |
| 4 | 294 | 0.56 | 0.76 | 32 | empty |
| 5 | 253 | 0.53 | 0.76 | 29 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1303 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1300 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 669 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 491 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 3WXG · Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin · the same entry in another collection · chain F against F, TM-score 1.00
- P0CG50 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG50) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0CG50
- Elsewhere: RCSB PDB 3WXG · PDBe 3WXG · UniProt E7FEV5 · UniProt P0CG50
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