Research workbench
Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin
Analyse Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FGE
- Type
- protein
- Length
- 418 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, NH4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger with UFM1-specific peptidase domain protein | protein | 343 | 47% helix, 17% strand | Q96AP4 |
| C | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · chains A, C
- NH4 · Ammonium ion · ion · 2 copies · chains A
- FMT · Formic acid · additive · 7 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MLI · Malonate ion · additive · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.61 | 0.87 | 24 | ACT |
| 2 | 69 | 0.58 | 0.89 | 16 | FMT |
| 3 | 110 | 0.52 | 0.82 | 23 | GOL, NH4 |
| 4 | 86 | 0.43 | 0.79 | 15 | empty |
| 5 | 57 | 0.36 | 0.79 | 16 | FMT |
Interfaces
1 interface between chains.
- A–C · 1397 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6FGE · Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin · 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 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 Q96AP4
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6FGE · PDBe 6FGE · UniProt Q96AP4 · UniProt P0CG47
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