Structure of PDB 7bgd Chain q Binding Site BS01

Receptor Information

>7bgd Chain q (length=86) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

SERNDRKVYVGKVVSDKMDKTITVLVETYKTHKLYGKRVKYSKKYKTHDE
NNSAKLGDIVKIQETRPLSATKRFRLVEIVEESVII

Ligand information

>7bgd Chain a (length=1096)

cuggagaguuugauccuggcucaggaugaacgcuggcggcgugccuaaua
caugcaagucgagcgaacggacgagaagcuugcuucucugauguuagcgg
cggacgggugaguaacacguggauaaccuaccuauaagacugggauaacu
ucgggaaaccguagcuaauaccggauaauauuuugaaccgcaugguucaa
aagugaaagacggucuugcugucacuuauagauggauccgcgcugcauua
gcuaguugguaagguaacggcuuaccaaggcaacgaugcauagccgaccu
gagagggugaucggccacacuggaacugagacacgguccagacuccuacg
ggaggcagcaguagggaaucuuccgcaaugggcgaaagccugacggagca
acgccgcgugagugaugaaggucuucggaucguaaaacucuguuauuagg
gaagaacauauguguaaguaacugugcacaucuugacgguaccuaaucag
aaagccacggcuaacuacgugccagcagccgcgguaauacguagguggca
agcguuauccggaauuauugggcguaaagcgcgcguaggcgguuuuuuaa
gucugaugugaaagcccacggcucaaccguggagggucauuggaaacugg
aaaacuugagugcagaagaggaaaguggaauuccauguguagcggugaaa
ugcgcagagauauggaggaacaccaguggcgaaggcgacuuucuggucug
uaacugacgcugaugugcgaaagcguggggaucaaacaggauuagauacc
cugguaguccacgccguaaacgaugagugcuaaguguuaggggguuuccc
gccccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacg
accgcaagguugaaacucaaaggaauugacggggaccgucuuguacacac
cgcccgucacaccacgagaguuuguaacacccgaagccgguggaguaacc
uuuuaggagcuagccgucgaaggugggacaaaugauuggggugaagucgu
aacaagguagccguaucggaaggugcggcuggaucaccuccuuucu

.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<
<.<<<..<<<..<<.<<<<......................>>>>.>>>>
>......<<........<<<<<<<..<<...<<<<<<<.<<<<.....<<
.<<<....>>>.>>......>>>>......<<<<<<<<<<..>>>>>>>>
>>......<<<<<<...>>>>>>.>>>>>>>..>>>>>>>>>.<<<....
<<<..<<<<<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<
....>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<<..>
>>>>...>>>>>>.........<<<....<<<<....>>>>..>>>..>>
.>>>>>>..<<<<......<<<<....>>>>.....>>>>...<<<<<<<
........<<.<<................>>.>.>......>>>>>>...
>..<<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>.
.>>>>>>>>>..........<<<((.....<<<<<..<<<.<<<<<<<.<
<<<<<<<<.......<<<<<<.....>>>>>>.....>>>>>>>..>>>>
>>>>>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......
>>>......>>>>>>>>...........<<....>>.>>>>>>>..>>>>
>.>>>...>>>..>>>>>....<<<<<<<...<...<<<<.<.....>.>
>>>...>>>>>>>>..........<<<<<<..<<<<<<<<<<<<<.....
>>>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<......<
<<<....>>>>....>>>..)))).]<<<<<.<<<<.>>>>>>>.>>...
.<..<<.<.<<<<.<<<..<<<<<<..<<<<....<.<<<<..<<<..<<
<...>>>.>>>.>>>>.>...>>>>..>>>>>>..>>>.>>>>..>.>>.
..>.....<<<<<<<<<....>>>>>>>>>................

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bgd Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S2 R4 N5 D6 R7 K8 Y10 K18 M19 D20 K21 T22 Y30 K31 T32 Y36 K38 K41 Y42 S43 K44 K45 Y46 K47 Q64 E65 T66 R67 P68 L69 S70 A71 K73 R74 R76
• Binding residue (residue number reindexed from 1): S1 R3 N4 D5 R6 K7 Y9 K17 M18 D19 K20 T21 Y29 K30 T31 Y35 K37 K40 Y41 S42 K43 K44 Y45 K46 Q63 E64 T65 R66 P67 L68 S69 A70 K72 R73 R75

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7bgd, PDBe:7bgd, PDBj:7bgd
• PDBsum: 7bgd
• UniProt: Q2FW15|RS17_STAA8 Small ribosomal subunit protein uS17 (Gene Name=rpsQ)