Research workbench
ADP-ribosyltransferase TOXIN/IMMUNITY pair
Analyse ADP-ribosyltransferase TOXIN/IMMUNITY pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DRE
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl-(dinitrogen reductase) hydrolase; Paar repeat-containing protein
- EC
- 3.2.2.24
- UniProt
- A8GG79, A8GG78
- Ligands
- MG
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl-(dinitrogen reductase) hydrolase (EC 3.2.2.24) | protein | 365 | 57% helix, 1% strand | A8GG79 |
| B | Paar repeat-containing protein | protein | 170 | 39% helix, 26% strand | A8GG78 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.59 | 0.82 | 21 | empty |
| 2 | 118 | 0.51 | 0.81 | 23 | empty |
| 3 | 139 | 0.46 | 0.77 | 24 | empty |
| 4 | 59 | 0.41 | 0.82 | 19 | empty |
| 5 | 65 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2698 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 6DRE · ADP-ribosyltransferase toxin/immunity pair · the same entry in another collection · chain A against A, TM-score 1.00
- A8GG79 · AlphaFold monomer V2.0 prediction for ADP-ribosylarginine hydrolase TRI1 (A8GG79) · a predicted model of the same protein · chain A against A, TM-score 0.97
- A8GG78 · AlphaFold monomer V2.0 prediction for NAD(+)--protein-arginine ADP- ribosyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 A8GG79
- Every structure of UniProt A8GG78
- Elsewhere: RCSB PDB 6DRE · PDBe 6DRE · UniProt A8GG79 · UniProt A8GG78
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