Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3. Determined by X-ray diffraction at 2.39 Å resolution. Released 10 Jul 2019.
Explore 6OQ7 in 3D Show helices and sheets RCSB PDB PDBe
6OQ7 contains 37 α-helices and 24 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 | 6-12 | 7 | |
| α-helix | 22-35 | 14 | |
| α-helix | 42-62 | 21 | |
| α-helix | 69-89 | 21 | |
| β-strand | 92-93 | 2 | 1 |
| α-helix | 94-95 | 2 | |
| β-strand | 97-101 | 5 | 2 |
| α-helix | 106-108 | 3 | |
| α-helix | 109-121 | 13 | |
| β-strand | 126-131 | 6 | 2 |
| α-helix | 138-156 | 19 | |
| α-helix | 158-160 | 3 | |
| α-helix | 168-196 | 29 | |
| α-helix | 202-214 | 13 | |
| α-helix | 218-233 | 16 | |
| β-strand | 237-239 | 3 | 2 |
| α-helix | 240-242 | 3 | |
| α-helix | 244-247 | 4 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 265-279 | 15 | |
| β-strand | 282-285 | 4 | 2 |
| β-strand | 290-291 | 2 | 3 |
| α-helix | 292 | 1 | |
| β-strand | 293 | 1 | 4 |
| α-helix | 294 | 1 | |
| α-helix | 302-304 | 3 | |
| α-helix | 310-325 | 16 | |
| α-helix | 334-337 | 4 | |
| α-helix | 341-353 | 13 | |
| α-helix | 357-360 | 4 | |
| β-strand | 361 | 1 | 4 |
| β-strand | 368-369 | 2 | 1 |
| β-strand | 375-379 | 5 | 2 |
| β-strand | 382-390 | 9 | 2 |
| α-helix | 395-419 | 25 | |
| α-helix | 425-438 | 14 | |
| α-helix | 445-448 | 4 | |
| α-helix | 454-456 | 3 | |
| α-helix | 466-469 | 4 | |
| α-helix | 472-484 | 13 | |
| α-helix | 496-499 | 4 | |
| α-helix | 500-502 | 3 | |
| β-strand | 503 | 1 | 2 |
| α-helix | 504-505 | 2 | |
| α-helix | 506-508 | 3 | |
| β-strand | 509-510 | 2 | 3 |
| α-helix | 515-517 | 3 | |
| α-helix | 525-540 | 16 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-7 | 4 | 5 |
| β-strand | 10-12 | 3 | 6 |
| β-strand | 18-24 | 7 | 5 |
| β-strand | 34-39 | 6 | 6 |
| β-strand | 46-51 | 6 | 6 |
| β-strand | 57-59 | 3 | 6 |
| β-strand | 67-71 | 5 | 5 |
| β-strand | 77-82 | 6 | 5 |
| α-helix | 87-89 | 3 | |
| β-strand | 91-96 | 6 | 6 |
| β-strand | 101 | 1 | 6 |
| β-strand | 105-109 | 5 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Toxin B | A | protein | 549 | Clostridioides difficile | Q9EXR0 (AlphaFold model) |
| E3 | C | protein | 137 | Camelidae |
>6OQ7_1 Toxin B (chains A) MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDTYI DTYKKSGRNKALKKFKEYLVIEILELKNSNLTPVEKNLHFIWIGGQINDTAINYINQWKD VNSDYNVNVFYDSNAFLINTLKKTIIESASNDTLESFRENLNDPEFNHTAFFRKRMQIIY DKQQNFINYYKAQKEENPDLIIDDIVKTYLSNEYSKDIDELNAYIEESLNKVTENSGNDV RNFEEFKTGEVFNLYEQELVERWNLAGASDILRVAILKNIGGVYLDVDMLPGIHPDLFKD INKPDSVKTAVDWEEMQLEAIMKHKEYIPEYTSKHFDTLDEEVQSSFESVLASKSDKSEI FLPLGDIEVSPLEVKIAFAKGSIINQALISAKDSYCSDLLIKQIQNRYKILNDTLGPIIS QGNDFNTTMNNFGESLGAIANEENISFIAKIGSYLRVGFYPEANTTITLSGPTIYAGAYK DLLTFKEMSIDTSILSSELRNFEFPKVNISQATEQEKNSLWQFNEERAKIQFEEYKKNYF EGAHHHHHH
>6OQ7_2 E3 (chains C) SNSQVQLVESGGGLVQTGGSLRLSCASSGSIAGFETVTWSRQAPGKSLQWVASMTKTNNE IYSDSVKGRFIISRDNAKNTVYLQMNSLKPEDTGVYFCKGPELRGQGIQVTVSSEPKTPK PQTSGAPVPYPDPLEPR
| ID | Name | Formula | Copies |
|---|---|---|---|
| UDP | Uridine-5'-diphosphate | C9 H14 N2 O12 P2 | 1 |
| GLC | alpha-D-glucopyranose | C6 H12 O6 | 1 |
| MN | Manganese (II) ion | Mn | 1 |
| MG | Magnesium ion | Mg | 1 |
Structure of the full-length Clostridium difficile toxin B. Chen, P., Lam, K.H., Liu, Z. et al. Nat Struct Mol Biol (2019) 26:712-719. DOI 10.1038/s41594-019-0268-0 · PubMed
Other PDB entries of the same protein (UniProt Q9EXR0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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