Crystal structure of SdeA catalytic core. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 May 2018.
Explore 6G0C in 3D Show helices and sheets RCSB PDB PDBe
6G0C contains 36 α-helices and 23 β-strands across 1 chain. 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 | 227-228 | 2 | |
| β-strand | 229 | 1 | 1 |
| α-helix | 238-250 | 13 | |
| α-helix | 255-256 | 2 | |
| α-helix | 263-264 | 2 | |
| β-strand | 265-267 | 3 | 2 |
| β-strand | 270-272 | 3 | 2 |
| α-helix | 279-302 | 24 | |
| α-helix | 315-317 | 3 | |
| α-helix | 320-331 | 12 | |
| α-helix | 344-364 | 21 | |
| α-helix | 377-388 | 12 | |
| α-helix | 391-393 | 3 | |
| α-helix | 398-408 | 11 | |
| α-helix | 409-413 | 5 | |
| α-helix | 418-451 | 34 | |
| α-helix | 455-457 | 3 | |
| β-strand | 459 | 1 | 3 |
| β-strand | 466 | 1 | 4 |
| α-helix | 467 | 1 | |
| β-strand | 468-469 | 2 | 5 |
| β-strand | 474-475 | 2 | 5 |
| β-strand | 477 | 1 | 6 |
| β-strand | 498 | 1 | 5 |
| β-strand | 513 | 1 | 6 |
| α-helix | 514 | 1 | |
| β-strand | 515 | 1 | 4 |
| α-helix | 516-521 | 6 | |
| α-helix | 523-526 | 4 | |
| β-strand | 536 | 1 | 3 |
| α-helix | 545-552 | 8 | |
| α-helix | 555-562 | 8 | |
| α-helix | 564-586 | 23 | |
| α-helix | 588-593 | 6 | |
| α-helix | 596-599 | 4 | |
| α-helix | 600-614 | 15 | |
| α-helix | 616-618 | 3 | |
| β-strand | 619 | 1 | 7 |
| β-strand | 624-626 | 3 | 7 |
| β-strand | 629-631 | 3 | 7 |
| α-helix | 633-642 | 10 | |
| α-helix | 645-650 | 6 | |
| α-helix | 654-666 | 13 | |
| β-strand | 671-672 | 2 | 8 |
| α-helix | 679-681 | 3 | |
| β-strand | 682-683 | 2 | 8 |
| α-helix | 684-691 | 8 | |
| α-helix | 702-713 | 12 | |
| α-helix | 716-726 | 11 | |
| α-helix | 735-756 | 22 | |
| β-strand | 763-768 | 6 | 1 |
| α-helix | 772-787 | 16 | |
| β-strand | 821-822 | 2 | 1 |
| α-helix | 825-826 | 2 | |
| α-helix | 827-831 | 5 | |
| β-strand | 836-841 | 6 | 1 |
| β-strand | 863 | 1 | 1 |
| β-strand | 871-881 | 11 | 1 |
| β-strand | 890-899 | 10 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitinating/deubiquitinating enzyme SdeA | A | protein | 695 | Legionella pneumophila | Q5ZTK4 (AlphaFold model) |
>6G0C_1 Ubiquitinating/deubiquitinating enzyme SdeA (chains A) EMSVKPTAPQDKSVPVWNGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMV YRQHHGLSHTLRTMAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAF FVAGRDDEASDAKNYQKYHEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSH DWESTPAHVLINQGHMVDLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHAT YEVVAGFDSDNKEPHLVVSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENER LMRVDEFLKLPEIQNTFPGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQ TAHDKAKIEPIKQAFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLE QQFFRDLLAKCEMAVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQ RINNSSGNITQKKHDLIFLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKAL VDTSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSK MSGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVA LVPVKVTLDGKTQKGENRYVFTFVAVKSPDFTPRH
| ID | Name | Formula | Copies |
|---|---|---|---|
| 1PS | 3-pyridinium-1-ylpropane-1-sulfonate | C8 H11 N O3 S | 1 |
Water and common crystallization additives (EDO) are not listed.
Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination. Kalayil, S., Bhogaraju, S., Bonn, F. et al. Nature (2018) 557:734-738. DOI 10.1038/s41586-018-0145-8 · PubMed
Other PDB entries of the same protein (UniProt Q5ZTK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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