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Crystal structure of sopd, a type III secreted virulence effector from salmonella enterica
Analyse Crystal structure of sopd, a type III secreted virulence effector from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CPC
- Type
- protein
- Length
- 561 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted effector protein sopd
- UniProt
- P40722
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secreted effector protein sopd | protein | 281 | 53% helix, 13% strand | P40722 |
| B | Secreted effector protein sopd | protein | 280 | 53% helix, 14% strand | P40722 |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.72 | 0.76 | 90 | empty |
| 2 | 166 | 0.48 | 0.77 | 17 | empty |
| 3 | 126 | 0.42 | 0.76 | 15 | empty |
| 4 | 96 | 0.41 | 0.77 | 19 | empty |
| 5 | 144 | 0.41 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5CPC · Crystal structure of SopD, a type III secreted virulence effector from Salmonella enterica · the same entry in another collection · chain A against A, TM-score 1.00
- P40722 · AlphaFold monomer V2.0 prediction for secreted effector protein sopd (P40722) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P40722
- Elsewhere: RCSB PDB 5CPC · PDBe 5CPC · UniProt P40722
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