Research workbench
A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak.
Analyse A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZJG
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.92
- Source
- HOMO SAPIENS
- Molecule
- Tumor necrosis factor alpha-induced protein 3
- EC
- 3.4.19.12, 6.3.2.-
- UniProt
- P21580
- Ligands
- CL
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.92 · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 327 | 40% helix, 19% strand | P21580 |
| B | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 328 | 38% helix, 19% strand | P21580 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.59 | 0.79 | 36 | empty |
| 2 | 184 | 0.50 | 0.77 | 27 | empty |
| 3 | 119 | 0.47 | 0.79 | 18 | empty |
| 4 | 56 | 0.42 | 0.82 | 14 | empty |
| 5 | 50 | 0.33 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 716 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3ZJG · A20 otu domain with irreversibly oxidised CYS103 from 60 min H2O2 soak. · the same entry in another collection · chain A against A, 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 B 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 P21580
- Elsewhere: RCSB PDB 3ZJG · PDBe 3ZJG · UniProt P21580
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