Research workbench
ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS
Analyse ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D0H
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Sphingobium sp. YBL2
- Molecule
- ParT: COG5654 (RES domain) toxin; ParS: COG5642 (DUF2384) antitoxin
- UniProt
- A0A0C5XL88, A0A0C5XKJ0
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.5 · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ParT: COG5654 (RES domain) toxin | protein | 160 | 23% helix, 28% strand | A0A0C5XL88 |
| B | ParS: COG5642 (DUF2384) antitoxin | protein | 72 | 65% helix, 4% strand | A0A0C5XKJ0 |
| C | ParT: COG5654 (RES domain) toxin | protein | 159 | 24% helix, 28% strand | A0A0C5XL88 |
| D | ParS: COG5642 (DUF2384) antitoxin | protein | 71 | 66% helix, 4% strand | A0A0C5XKJ0 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
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 | 320 | 0.63 | 0.80 | 47 | empty |
| 2 | 117 | 0.53 | 0.82 | 18 | empty |
| 3 | 92 | 0.47 | 0.81 | 20 | empty |
| 4 | 92 | 0.36 | 0.75 | 18 | empty |
| 5 | 73 | 0.35 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1408 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1367 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 809 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 230 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 185 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6D0H · Part: prs ADP-ribosylating toxin bound to cognate antitoxin pars · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0C5XL88
- Every structure of UniProt A0A0C5XKJ0
- Elsewhere: RCSB PDB 6D0H · PDBe 6D0H · UniProt A0A0C5XL88 · UniProt A0A0C5XKJ0
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