MolNFT v2 · #84421 · protein
A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak.
3ZJG · Tumor necrosis factor alpha-induced protein 3: “A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak.”. X-ray diffraction at 1.92, 1 ligand (CL), 7 pockets (best druggability 0.59). MolNFT v2 #84421 on GenesisL1…
- 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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