MolNFT v1 · #84393 · protein
A20 otu domain with irreversibly oxidised CYS103 from 270 min H2O2 soak.
3ZJF · A20P50: “A20 otu domain with irreversibly oxidised CYS103 from 270 min H2O2 soak.”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.60). MolNFT v1 #84393 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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