Research workbench
A20 otu domain with irreversibly oxidised CYS103 from 270 min H2O2 soak.
Analyse A20 otu domain with irreversibly oxidised CYS103 from 270 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
- 3ZJF
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A20P50
- EC
- 3.4.19.12, 6.3.2.-
- UniProt
- P21580
- Ligands
- CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A20P50 (EC 3.4.19.12, 6.3.2.-) | protein | 323 | 41% helix, 19% strand | P21580 |
| B | A20P50 (EC 3.4.19.12, 6.3.2.-) | protein | 322 | 40% helix, 19% strand | P21580 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.60 | 0.79 | 46 | empty |
| 2 | 149 | 0.56 | 0.82 | 37 | empty |
| 3 | 158 | 0.50 | 0.78 | 27 | empty |
| 4 | 70 | 0.42 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3ZJF · A20 OTU domain with irreversibly oxidised Cys103 from 270 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 3ZJF · PDBe 3ZJF · UniProt P21580
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