Crystal structure of SopD, a type III secreted virulence effector from Salmonella enterica. Determined by X-ray diffraction at 2.15 Å resolution. Released 9 Sept 2015.
Explore 5CPC in 3D Show helices and sheets RCSB PDB PDBe
5CPC contains 38 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 34-36 | 3 | |
| α-helix | 37-40 | 4 | |
| α-helix | 41-43 | 3 | |
| α-helix | 46-48 | 3 | |
| α-helix | 49-60 | 12 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73 | 1 | 1 |
| α-helix | 76-90 | 15 | |
| α-helix | 93-98 | 6 | |
| β-strand | 99-103 | 5 | 2 |
| β-strand | 109-114 | 6 | 2 |
| β-strand | 117-123 | 7 | 2 |
| α-helix | 124-127 | 4 | |
| α-helix | 141-160 | 20 | |
| α-helix | 163-167 | 5 | |
| α-helix | 169-177 | 9 | |
| α-helix | 180-190 | 11 | |
| α-helix | 199-200 | 2 | |
| β-strand | 201-202 | 2 | 3 |
| α-helix | 203 | 1 | |
| α-helix | 209-215 | 7 | |
| α-helix | 216-219 | 4 | |
| β-strand | 232-237 | 6 | 4 |
| β-strand | 240-245 | 6 | 4 |
| α-helix | 248-251 | 4 | |
| α-helix | 252-256 | 5 | |
| β-strand | 260 | 1 | 1 |
| α-helix | 264-283 | 20 | |
| α-helix | 285-298 | 14 | |
| β-strand | 305-306 | 2 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 34-36 | 3 | |
| α-helix | 37-40 | 4 | |
| α-helix | 41-43 | 3 | |
| α-helix | 46-48 | 3 | |
| α-helix | 49-60 | 12 | |
| β-strand | 73 | 1 | 5 |
| α-helix | 76-90 | 15 | |
| α-helix | 93-98 | 6 | |
| β-strand | 99-103 | 5 | 6 |
| β-strand | 109-114 | 6 | 6 |
| β-strand | 117-123 | 7 | 6 |
| α-helix | 124-127 | 4 | |
| α-helix | 141-160 | 20 | |
| α-helix | 162-167 | 6 | |
| α-helix | 169-177 | 9 | |
| α-helix | 180-190 | 11 | |
| β-strand | 201-202 | 2 | 7 |
| α-helix | 209-215 | 7 | |
| α-helix | 216-219 | 4 | |
| β-strand | 232-237 | 6 | 8 |
| β-strand | 240-245 | 6 | 8 |
| α-helix | 248-255 | 8 | |
| β-strand | 260 | 1 | 5 |
| α-helix | 264-283 | 20 | |
| α-helix | 285-298 | 14 | |
| β-strand | 305-306 | 2 | 7 |
| β-strand | 307 | 1 | 9 |
| β-strand | 310 | 1 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Secreted effector protein SopD | A, B | protein | 317 | Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) | P40722 (AlphaFold model) |
>5CPC_1 Secreted effector protein SopD (chains A, B) MPVTLSFGNHQNYTLNESRLAHLLSADKEKAIHMGGWDKVQDHFRAEKKDHALEVLHSII HGQGRGEPGEMEVNVEDINKIYAFKRLQHLACPAHQDLFTIKMDASQTQFLLMVGDTVIS QSNIKDILNISDDAVIESMSREERQLFLQICEVIGSKMTWHPELLQESISTLRKEVTGNA QIKTAVYEMMRPAEAPDHPLVEWQDSLTADEKSMLACINAGNFEPTTQFCKIGYQEVQGE VAFSMMHPCISYLLHSYSPFSEFKPTNSGFLKKLNQDYNDYHAKKMFIDVILEKLYLTHE RSLHIGKDGCSRNILLT
Salmonella Disrupts Host Endocytic Trafficking by SopD2-Mediated Inhibition of Rab7. D'Costa, V.M., Braun, V., Landekic, M. et al. Cell Rep (2015) 12:1508-1518. DOI 10.1016/j.celrep.2015.07.063 · PubMed
Other PDB entries of the same protein (UniProt P40722 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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