MolNFT v2 · #228861 · protein
Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex (VapB T3N, A13P, L16R)
9H6B · tRNA(fMet)-specific endonuclease VapC: “Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex (VapB T3N, A13P, L16R)”. X-ray diffraction at 2.8, 3 pockets (best druggability 0.39). MolNFT v2 #228861 on GenesisL1…
- PDB
- 9H6B
- Type
- protein
- Length
- 403 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Escherichia coli KLY
- Molecule
- tRNA(fMet)-specific endonuclease VapC; Antitoxin
- EC
- 3.1.-.-
- UniProt
- Q84A22, Q7B3V0
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | tRNA(fMet)-specific endonuclease VapC (EC 3.1.-.-) | protein | 132 | 58% helix, 14% strand | Q84A22 |
| B | Antitoxin | protein | 70 | 11% helix, 23% strand | Q7B3V0 |
| D | Antitoxin | protein | 69 | 7% helix, 23% strand | Q7B3V0 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.39 | 0.74 | 31 | empty |
| 2 | 106 | 0.38 | 0.75 | 21 | empty |
| 3 | 68 | 0.30 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1590 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1473 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 121 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 93 Ų buried · 1 hydrogen bond · protein-protein
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 Q84A22
- Every structure of UniProt Q7B3V0
- Elsewhere: RCSB PDB 9H6B · PDBe 9H6B · UniProt Q84A22 · UniProt Q7B3V0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.