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Structure of the chromobacterium violaceum vira (spvc) phosphothreonine lyase effector protein
Analyse Structure of the chromobacterium violaceum vira (spvc) phosphothreonine lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO6
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrophilic protein, vira protein
- EC
- 4.2.3.-
- UniProt
- Q7NYG6
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrophilic protein, vira protein (EC 4.2.3.-) | protein | 220 | 33% helix, 19% strand | Q7NYG6 |
| B | Hydrophilic protein, vira protein (EC 4.2.3.-) | protein | 215 | 33% helix, 17% strand | Q7NYG6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 180 | 0.52 | 0.79 | 27 | empty |
| 2 | 187 | 0.52 | 0.78 | 33 | SO4 |
| 3 | 100 | 0.48 | 0.81 | 23 | SO4 |
| 4 | 66 | 0.31 | 0.75 | 21 | empty |
| 5 | 56 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3BO6 · Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector… · 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 Q7NYG6
- Elsewhere: RCSB PDB 3BO6 · PDBe 3BO6 · UniProt Q7NYG6
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