Research workbench
Part: prs ADP-ribosylating toxin bound to cognate antitoxin pars. L48M part, semet-substituted complex.
Analyse Part: prs ADP-ribosylating toxin bound to cognate antitoxin pars. L48M part… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D0I
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Part: COG5654 (res domain) toxin; Pars: COG5642 (DUF2384) antitoxin fragment
- UniProt
- A0A0C5XL88, A0A0C5XKJ0
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 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 fragment | 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 fragment | protein | 71 | 66% helix, 4% strand | A0A0C5XKJ0 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.64 | 0.83 | 32 | empty |
| 2 | 93 | 0.51 | 0.83 | 18 | empty |
| 3 | 73 | 0.43 | 0.81 | 18 | empty |
| 4 | 158 | 0.43 | 0.74 | 27 | empty |
| 5 | 78 | 0.35 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1376 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1374 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 825 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6D0I · ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS. L48M ParT… · 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 6D0I · PDBe 6D0I · UniProt A0A0C5XL88 · UniProt A0A0C5XKJ0
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