Research workbench
Structure of vapbc from shigella sonnei
Analyse Structure of vapbc from shigella sonnei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SD6
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin; TRNA(FMET)-specific endonuclease vapc
- EC
- 3.1.-.-
- UniProt
- A0A3U1ZEK5, A0A0H9P9N5
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antitoxin | protein | 68 | 7% helix, 29% strand | A0A3U1ZEK5 |
| B | Antitoxin | protein | 67 | 7% helix, 18% strand | A0A3U1ZEK5 |
| C | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 135 | 56% helix, 12% strand | A0A0H9P9N5 |
| D | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 54% helix, 14% strand | A0A0H9P9N5 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.33 | 0.73 | 20 | empty |
| 2 | 55 | 0.29 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1565 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1481 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1112 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SD6 · Structure of VapBC from Shigella sonnei · 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 A0A3U1ZEK5
- Every structure of UniProt A0A0H9P9N5
- Elsewhere: RCSB PDB 6SD6 · PDBe 6SD6 · UniProt A0A3U1ZEK5 · UniProt A0A0H9P9N5
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