Research workbench
Structure of dub complex
Analyse Structure of dub complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VSK
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 3.4.19.12
- UniProt
- Q93009
- Ligands
- 9HS, ZN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 330 | 32% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 305 | 31% helix, 22% strand | Q93009 |
Ligands and binding sites
- 9HS · 7-chloro-3-({4-hydroxy-1-[(3S)-3-phenylbutanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.72 | 0.87 | 25 | 9HS |
| 2 | 894 | 0.72 | 0.76 | 77 | empty |
| 3 | 273 | 0.65 | 0.82 | 28 | 9HS |
| 4 | 55 | 0.49 | 0.85 | 16 | empty |
| 5 | 144 | 0.48 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 221 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VSK · Structure of DUB complex · 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 Q93009
- Elsewhere: RCSB PDB 5VSK · PDBe 5VSK · UniProt Q93009
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