MolNFT v1 · #137555 · protein
Structure of dub complex
5VS6 · Ubiquitin carboxyl-terminal hydrolase 7: “Structure of dub complex”. X-ray diffraction, 1 ligand (9QD), 9 pockets (best druggability 0.72). MolNFT v1 #137555 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VS6
- Type
- protein
- Length
- 676 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
- 9QD
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 339 | 34% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 337 | 34% helix, 27% strand | Q93009 |
Ligands and binding sites
- 9QD · N-[3-({4-hydroxy-1-[(3R)-3-phenylbutanoyl]piperidin-4-yl}methyl)-4-oxo-3,4-dihydroquinazolin-7-yl]-3-(4-methylpiperazin-1-yl)propanamide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 307 | 0.72 | 0.85 | 56 | empty |
| 2 | 195 | 0.71 | 0.88 | 25 | 9QD, ACT |
| 3 | 202 | 0.70 | 0.87 | 26 | 9QD, ACT, GOL |
| 4 | 129 | 0.45 | 0.77 | 20 | empty |
| 5 | 73 | 0.41 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VS6 · 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 5VS6 · PDBe 5VS6 · UniProt Q93009
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.