Research workbench
Structure of virulence-associated protein D (vapd) from xylella fastidiosa
Analyse Structure of virulence-associated protein D (vapd) from xylella fastidiosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DYR
- Type
- protein
- Length
- 139 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virulence-associated protein D
- UniProt
- Q9PHF6
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence-associated protein D | protein | 139 | 55% helix, 0% strand | Q9PHF6 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.65 | 0.79 | 35 | empty |
| 2 | 86 | 0.37 | 0.76 | 18 | empty |
Compared structures
- 5DYR · Structure of virulence-associated protein D (VapD) from Xylella fastidiosa · 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 Q9PHF6
- Elsewhere: RCSB PDB 5DYR · PDBe 5DYR · UniProt Q9PHF6
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