MolNFT v1 · #146948 · protein
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-YL)PROPANOATE
6DXT · Ubiquitin carboxyl-terminal hydrolase 5: “Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with…”. X-ray diffraction, 3 ligands (HHY, ZN, UNX), 3 pockets (best druggability 0.35). MolNFT v1 #146948 on…
- PDB
- 6DXT
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 5
- EC
- 3.4.19.12
- UniProt
- P45974
- Ligands
- HHY, ZN, UNX
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 112 | 13% helix, 21% strand | P45974 |
| B | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 115 | 13% helix, 20% strand | P45974 |
Ligands and binding sites
- HHY · 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.35 | 0.79 | 10 | HHY |
| 2 | 59 | 0.34 | 0.77 | 14 | empty |
| 3 | 56 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6DXT · Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with… · the same entry in another collection · chain A against A, TM-score 1.00
- P45974 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 5 (P45974) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P45974
- Elsewhere: RCSB PDB 6DXT · PDBe 6DXT · UniProt P45974
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