Research workbench
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (5-((4-(4-chlorophenyl)piperidin-1-yl)sulfonyl)picolinoyl)glycine
Analyse Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MS7
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Homo sapiens
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 5
- EC
- 3.4.19.12
- UniProt
- P45974
- Ligands
- ZQ1, ZN
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · resolution 1.45 · 2 distinct chains · 13% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 113 | 13% helix, 20% strand | P45974 |
| B | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 114 | 13% helix, 18% strand | P45974 |
Ligands and binding sites
- ZQ1 · N-{5-[4-(4-chlorophenyl)piperidine-1-sulfonyl]pyridine-2-carbonyl}glycine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MS7 · 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 0.98
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 P45974
- Elsewhere: RCSB PDB 7MS7 · PDBe 7MS7 · UniProt P45974
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