Research workbench
Crystal structure of the A20 ZNF4, ubiquitin and UBCH5A complex
Analyse Crystal structure of the A20 ZNF4, ubiquitin and UBCH5A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJ4
- Type
- protein
- Length
- 500 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D1; Ubiquitin; Tumor necrosis factor alpha-induced…
- EC
- 6.3.2.19
- UniProt
- P51668, P0CG47, P21580
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 147 | 37% helix, 21% strand | P51668 |
| B, E | Ubiquitin | protein | 72 | 25% helix, 36% strand | P0CG47 |
| C, F | Tumor necrosis factor alpha-induced protein 3 | protein | 31 | 42% helix, 6% strand | P21580 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.66 | 0.84 | 32 | empty |
| 2 | 223 | 0.66 | 0.84 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 731 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 722 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 408 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OJ4 · Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex · the same entry in another collection · chain F against F, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P51668
- Every structure of UniProt P0CG47
- Every structure of UniProt P21580
- Elsewhere: RCSB PDB 3OJ4 · PDBe 3OJ4 · UniProt P51668 · UniProt P0CG47 · UniProt P21580
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