Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii with antibiotic thiostrepton. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Aug 2016.
Explore 5D8H in 3D Show helices and sheets RCSB PDB PDBe
5D8H contains 19 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 | 11-26 | 16 | |
| β-strand | 29-34 | 6 | 1 |
| α-helix | 40-49 | 10 | |
| β-strand | 54-58 | 5 | 1 |
| α-helix | 61-74 | 14 | |
| α-helix | 78-82 | 5 | |
| α-helix | 83-86 | 4 | |
| β-strand | 91-96 | 6 | 1 |
| α-helix | 100-109 | 10 | |
| β-strand | 112-114 | 3 | 2 |
| β-strand | 121 | 1 | 3 |
| β-strand | 131-132 | 2 | 4 |
| α-helix | 141-143 | 3 | |
| β-strand | 151-154 | 4 | 4 |
| β-strand | 157-160 | 4 | 4 |
| β-strand | 172 | 1 | 3 |
| α-helix | 173-174 | 2 | |
| α-helix | 175-183 | 9 | |
| β-strand | 189-191 | 3 | 2 |
| β-strand | 194-200 | 7 | 1 |
| β-strand | 203-205 | 3 | 1 |
| α-helix | 207-211 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-10 | 9 | 5 |
| α-helix | 20-24 | 5 | |
| α-helix | 25-27 | 3 | |
| α-helix | 33-41 | 9 | |
| α-helix | 43-45 | 3 | |
| β-strand | 49-57 | 9 | 5 |
| β-strand | 65-67 | 3 | 5 |
| α-helix | 72-77 | 6 | |
| β-strand | 89 | 1 | 6 |
| β-strand | 92 | 1 | 6 |
| β-strand | 96-97 | 2 | 7 |
| α-helix | 99-109 | 11 | |
| α-helix | 110-112 | 3 | |
| α-helix | 118-130 | 13 | |
| β-strand | 135-136 | 2 | 7 |
| β-strand | 139 | 1 | 7 |
| α-helix | 141-149 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| 23S ribosomal RNA | A | RNA | 74 | Methanocaldococcus jannaschii | |
| 50S ribosomal protein L10 | B | protein | 213 | Methanocaldococcus jannaschii | P54049 (AlphaFold model) |
| 50S ribosomal protein L11 | C | protein | 161 | Methanocaldococcus jannaschii | P54030 (AlphaFold model) |
| Thiostrepton | D | protein | 19 | Streptomyces azureus | P0C8P8 (AlphaFold model) |
>5D8H_1 23S ribosomal RNA (chains A) GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGC UCACCCGUCGAGGC
>5D8H_2 50S ribosomal protein L10 (chains B) MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRAL KEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKV EKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKP IKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI
>5D8H_3 50S ribosomal protein L11 (chains C) MAKEVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVDTE TRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSYTLK NAVKEVLGTCGSMGVTVEGKDPKEVQKEIDAGVYDEYFKEE
>5D8H_4 THIOSTREPTON (chains D) XIASASCTTCICTCSCSSX
| ID | Name | Formula | Copies |
|---|---|---|---|
| MG | Magnesium ion | Mg | 11 |
Water and common crystallization additives (TRS, NA) are not listed.
CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON. Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B. To be published.
Other PDB entries of the same protein (UniProt P54049 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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