Research workbench
Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II
Analyse Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VUX
- Type
- protein
- Length
- 327 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C; Tumor necrosis factor alpha-induced protein 3
- UniProt
- P0CG48, P21580
- Ligands
- ZN, K
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polyubiquitin-C | protein | 76 | 24% helix, 33% strand | P0CG48 |
| E | Tumor necrosis factor alpha-induced protein 3 | protein | 33 | 36% helix, 6% strand | P21580 |
| F | Tumor necrosis factor alpha-induced protein 3 | protein | 32 | 41% helix, 6% strand | P21580 |
| G | Tumor necrosis factor alpha-induced protein 3 | protein | 34 | 29% helix, 6% strand | P21580 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B, E, C, F, A, G
- K · Potassium ion · metal · 3 copies · chains E, F, G
- EDO · 1,2-ethanediol · additive · chains A, G
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 | 69 | 0.33 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–G · 637 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 622 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 616 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 395 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 334 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VUX · Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II · the same entry in another collection · chain B against B, TM-score 1.00
- P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain F against A, TM-score 0.89
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 P0CG48
- Every structure of UniProt P21580
- Elsewhere: RCSB PDB 3VUX · PDBe 3VUX · UniProt P0CG48 · UniProt P21580
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