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
- 6DRH
- Type
- protein
- Length
- 2,194 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.299
- Source
- Serratia proteamaculans (strain 568)
- Molecule
- ADP-ribosyl-(Dinitrogen reductase) hydrolase; PAAR repeat-containing protein
- EC
- 3.2.2.24
- UniProt
- A8GG79, A8GG78
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.299 · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | ADP-ribosyl-(Dinitrogen reductase) hydrolase (EC 3.2.2.24) | protein | 365 | 59% helix, 1% strand | A8GG79 |
| B, D, H | PAAR repeat-containing protein | protein | 185 | 38% helix, 23% strand | A8GG78 |
| E | ADP-ribosyl-(Dinitrogen reductase) hydrolase (EC 3.2.2.24) | protein | 366 | 58% helix, 1% strand | A8GG79 |
| F | PAAR repeat-containing protein | protein | 178 | 37% helix, 25% strand | A8GG78 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.76 | 0.79 | 107 | empty |
| 2 | 982 | 0.75 | 0.78 | 69 | empty |
| 3 | 627 | 0.71 | 0.79 | 68 | PO4 |
| 4 | 559 | 0.70 | 0.79 | 62 | empty |
| 5 | 787 | 0.69 | 0.75 | 64 | empty |
Interfaces
15 interfaces between chains.
- G–H · 2735 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2709 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2688 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2669 Ų buried · 43 hydrogen bonds · protein-protein
- A–F · 476 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DRH · ADP-ribosyltransferase TOXIN/IMMUNITY pair · the same entry in another collection · chain H against H, 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 F 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 6DRH · PDBe 6DRH · UniProt A8GG79 · UniProt A8GG78
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