MolNFT v1 · #147595 · protein
Crystal structure of the covalent complex between deubiquitinase zufsp (ZUP1) and ubiquitin-pa
6EI1 · Zinc finger with UFM1-specific peptidase domain protein: “Crystal structure of the covalent complex between deubiquitinase zufsp (ZUP1) and ubiquitin-pa”. X-ray diffraction, 1 ligand (AYE), 4 pockets (best druggability 0.61). MolNFT…
- PDB
- 6EI1
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger with UFM1-specific peptidase domain protein; Polyubiquitin-B
- UniProt
- Q96AP4, P0CG47
- Ligands
- AYE
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger with UFM1-specific peptidase domain protein | protein | 335 | 47% helix, 19% strand | Q96AP4 |
| B | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · chains A, B
- GOL · Glycerol · additive · chains A
- MLI · Malonate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.61 | 0.91 | 15 | empty |
| 2 | 98 | 0.59 | 0.86 | 22 | empty |
| 3 | 113 | 0.52 | 0.82 | 25 | empty |
| 4 | 51 | 0.35 | 0.79 | 17 | MLI |
Interfaces
1 interface between chains.
- A–B · 1361 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6EI1 · Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96AP4 · AlphaFold monomer V2.0 prediction for zinc finger-containing ubiquitin peptidase 1… · a predicted model of the same protein · 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 Q96AP4
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6EI1 · PDBe 6EI1 · UniProt Q96AP4 · UniProt P0CG47
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