Research workbench
Crystal structure of shigella flexneri vapbc toxin-antitoxin complex
Analyse Crystal structure of shigella flexneri vapbc toxin-antitoxin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TND
- Type
- protein
- Length
- 797 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc; Antitoxin vapb
- EC
- 3.1.-.-
- UniProt
- O06662, O06663
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 59% helix, 14% strand | O06662 |
| B, D | Antitoxin vapb | protein | 68 | 12% helix, 34% strand | O06663 |
| F | Antitoxin vapb | protein | 66 | 12% helix, 27% strand | O06663 |
| H | Antitoxin vapb | protein | 67 | 10% helix, 34% strand | O06663 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, E, F, C, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.69 | 0.79 | 62 | empty |
| 2 | 431 | 0.67 | 0.79 | 64 | empty |
| 3 | 60 | 0.30 | 0.75 | 15 | empty |
| 4 | 74 | 0.29 | 0.72 | 21 | empty |
| 5 | 63 | 0.28 | 0.73 | 15 | empty |
Interfaces
19 interfaces between chains.
- F–H · 1616 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1587 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1561 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1543 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1462 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3TND · Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex · the same entry in another collection · chain H against H, TM-score 1.00
- O06662 · AlphaFold monomer V2.0 prediction for TRNA(FMET)-specific endonuclease vapc (O06662) · a predicted model of the same protein · chain A against A, TM-score 0.96
- O06663 · AlphaFold monomer V2.0 prediction for antitoxin vapb (O06663) · a predicted model of the same protein · chain H against A, TM-score 0.82
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 O06662
- Every structure of UniProt O06663
- Elsewhere: RCSB PDB 3TND · PDBe 3TND · UniProt O06662 · UniProt O06663
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