Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1. Determined by X-ray diffraction at 2.15 Å resolution. Released 12 Apr 2023.
Explore 8ALK in 3D Show helices and sheets RCSB PDB PDBe
8ALK contains 27 α-helices and 36 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 |
|---|---|---|---|
| β-strand | 22-24 | 3 | 1 |
| α-helix | 25-27 | 3 | |
| β-strand | 29-32 | 4 | 2 |
| α-helix | 35-38 | 4 | |
| α-helix | 43-50 | 8 | |
| β-strand | 51-57 | 7 | 3 |
| β-strand | 60-66 | 7 | 3 |
| β-strand | 69 | 1 | 4 |
| β-strand | 75-79 | 5 | 2 |
| β-strand | 82-90 | 9 | 1 |
| β-strand | 96-106 | 11 | 1 |
| α-helix | 114-133 | 20 | |
| α-helix | 138-146 | 9 | |
| β-strand | 166-176 | 11 | 1 |
| β-strand | 180-188 | 9 | 1 |
| β-strand | 192-196 | 5 | 3 |
| β-strand | 202-206 | 5 | 3 |
| β-strand | 208-212 | 5 | 5 |
| β-strand | 217-219 | 3 | 5 |
| β-strand | 237-243 | 7 | 1 |
| β-strand | 248-252 | 5 | 3 |
| α-helix | 254-257 | 4 | |
| β-strand | 262-267 | 6 | 5 |
| β-strand | 271-276 | 6 | 5 |
| α-helix | 278-282 | 5 | |
| α-helix | 285-288 | 4 | |
| α-helix | 296-327 | 32 | |
| α-helix | 330-332 | 3 | |
| β-strand | 337 | 1 | 6 |
| α-helix | 338-347 | 10 | |
| α-helix | 351-362 | 12 | |
| β-strand | 371-372 | 2 | 7 |
| β-strand | 379 | 1 | 6 |
| α-helix | 380-389 | 10 | |
| β-strand | 392 | 1 | 4 |
| β-strand | 395-402 | 8 | 3 |
| α-helix | 403-405 | 3 | |
| α-helix | 406-416 | 11 | |
| α-helix | 418-420 | 3 | |
| α-helix | 421-424 | 4 | |
| α-helix | 425-430 | 6 | |
| α-helix | 435-447 | 13 | |
| β-strand | 449-450 | 2 | 8 |
| β-strand | 455-457 | 3 | 3 |
| α-helix | 458-460 | 3 | |
| β-strand | 464-465 | 2 | 8 |
| α-helix | 469-482 | 14 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 7-14 | 8 | 9 |
| α-helix | 21-29 | 9 | |
| β-strand | 45-52 | 8 | 9 |
| β-strand | 55-63 | 9 | 9 |
| α-helix | 67-69 | 3 | |
| β-strand | 71-72 | 2 | 7 |
| β-strand | 73-74 | 2 | 5 |
| β-strand | 83-89 | 7 | 9 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 9 |
| α-helix | 133-142 | 10 | |
| β-strand | 147-149 | 3 | 9 |
| β-strand | 151 | 1 | 10 |
| β-strand | 156 | 1 | 10 |
| α-helix | 158-172 | 15 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Phosphocholine hydrolase Lem3 | A | protein | 469 | Legionella pneumophila | Q5ZXN5 (AlphaFold model) |
| Ras-related protein Rab-1B | B | protein | 175 | Homo sapiens | Q9H0U4 (AlphaFold model) |
>8ALK_1 Phosphocholine hydrolase Lem3 (chains A) GHMDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEH DTILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNSDQN IDTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGDGLIIILD KRFKIKHMVSASHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVW GELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKT LIKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIE IPLEMVMHDLKSRCVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEAD LEEAFHRLSLEMVQPEIESPISETHFERAFKKETLDKTQAVLTHYFRIS
>8ALK_2 Ras-related protein Rab-1B (chains B) GPMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKL QIWDTAGQERFRTITSTYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLV GNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMG
| ID | Name | Formula | Copies |
|---|---|---|---|
| OJU | 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]m… | C18 H33 Cl N5 O12 P2 | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| CA | Calcium ion | Ca | 4 |
Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b. Kaspers, M.S., Pogenberg, V., Pett, C. et al. Nat Commun (2023) 14:2245-2245. DOI 10.1038/s41467-023-37621-7 · PubMed
Other PDB entries of the same protein (UniProt Q5ZXN5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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