Structure of PDB 6spd Chain C Binding Site BS01

Receptor Information

>6spd Chain C (length=271) Species: 287 (Pseudomonas aeruginosa)

IVKCKPTSAGRRFVVKVVNQELHKGAPYAPLLEKKSKSGGRNNNGRITTR
HIGGGHKQHYRLVDFRRNKDGIPAIVERVEYDPNRTAHIALLKYADGERR
YIIAPKGVAAGDQLISGIGAPIKAGNSMPLRNIPVGSTVHGIELKPGKGA
QIARSAGASAQLVAREGAYVTLRLRSGEMRKVLAECRATLGEVSNSEHSL
RSLGKAGATRWRGVRPTVRGVAMNPVDHPHGGGEGRTSAGRHPVSPWGLQ
TKGKKTRSNKRTDNMIVRRRK

Ligand information

>6spd Chain A (length=2851)

gucaagugaagaagcgcauacgguggaugccuuggcagucagaggcgaug
aaagacgugguagccugcgaaaagcuucggggagucggcaaacagacuuu
gauccggagaucucugaaugggggaacccaccuaggauaaccuagguauc
uuguacugaauccauaggugcaagaggcgaaccaggggaacugaaacauc
uaaguacccugaggaaaagaaaucaaccgagauucccuuaguaguggcga
gcgaacggggauuagcccuuaagcuauuuuagcggaacgcucuggaaagu
gcggccauagugggugauagccccguacgcgaaaggaucuuugaagugaa
aucaaguaggacggagcacgagaaacuuugucugaacauggggggaccau
ccuccaaggcuaaauacuacugacugaccgauagugaaccaguaccguga
gggaaaggcgaaaagaaccccggagaggggagugaaauagaccugaaacc
guaugcguacaagcagugggagccuacuuguuaggugacugcguaccuuu
uguauaaugggucagcgacuuauauucaguggcaagcuuaaccguauagg
guaggcguagcgaaagcgagucuuaauagggcguagucgcuggguauaga
cccgaaaccgggcgaucuauccaugagcagguugaagguuagguaacacu
gacuggaggaccgaacccacucccguugaaaagguaggggaugacuugug
gaucggagugaaaggcuaaucaagcucggagauagcugguucuccucgaa
agcuauuuagguagcgccucauguaucacucugggggguagagcacuguu
ucggcuagggggucaucccgacuuaccaaaccgaugcaaacuccgaauac
ccagaagugagcaugggagacacacggcgggugcuaacguccgucgugaa
aagggaaacaacccagaccgccagcuaaggucccaaaguugugguuaagu
gguaaacgaugugggaaggcuuagacagcuaggagguuggcuuagaagca
gccacccuuuaaagaaagcguaauagcucacuagucgagucggccugcgc
ggaagauguaacggggcaaccacacaccgaagcugcgggugucacguaag
ugacgcgguagaggagcguucuguaagccugugaaggugaguugagaagc
uugcuggagguaucagaagugcgaaugcugacaugaguaacgacaauggg
ugugaaaaacacccacgccgaaagaccaaggguuccugcgcaacguuaau
cgacgcaggguuagucgguuccuaaggcgaggcugaaaagcguagucgau
gggaaacagguuaauauuccuguacuucugguuacugcgauggagggacg
gagaaggcuaggccagcuuggcguugguuguccaaguuuaaggugguagg
cugaaaucuuagguaaauccgggguuucaaggccgagagcugaugacgag
ucguagaugacgaagugguugaugccaugcuuccaagaaaagcuucuaag
cuucagguaaccaggaaccguaccccaaaccgacacagguggucggguag
agaauaccaaggcgcuugagagaacucgggugaaggaacuaggcaaaaug
gcaccguaacuucgggagaaggugcgccggcuagugaaaagcucuggcug
gucgaagauaccaggccgcugcgacuguuuauuaaaaacacagcacucug
caaacacgaaaguggacguauagggugugacgccugcccggugccggaag
guuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccggua
aacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgg
guaaguuccgaccugcacgaauggcguaacgauggcggcgcugucuccac
ccgagacucagugaaauugaaaucgcugugaagaugcaguguauccgcgg
cuagacggaaagaccccgugaaccuuuacuguagcuuugcacuggacuuu
gagccugcuuguguaggauaggugggaggcuuugaagcguggacgccagu
ucgcguggagccauccuugaaauaccacccuggcaugcuugagguucuaa
cucugguccguaauccggaucgaggacaguguauggugggcaguuugacu
ggggcggucuccuccuaaagaguaacggaggaguacgaaggugcgcucag
accggucggaaaucggucgcagaguauaaaggcaaaagcgcgcuugacug
cgagacagacacgucgagcagguacgaaaguaggucuuagugauccggug
guucuguauggaagggccaucgcucaacggauaaaagguacuccggggau
aacaggcugauaccgcccaagaguucauaucgacggcgguguuuggcacc
ucgaugucggcucaucacauccuggggcugaagccggucccaaggguaug
gcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugag
acaguucggucccuaucugccguggacguuugagauuugagaggggcugc
uccuaguacgagaggaccggaguggacgaaccucuggguuccgguuguca
cgccaguggcauugccggguagcuauguucggaaaagauaaccgcugaaa
gcaucuaagcgggaaacuugccucaagaugagaucucacugggaacuuga
uuccccugaagggccgucgaagacuacgacguugauaggcugggugugua
agcguugugaggcguugagcuaaccaguacuaaugcccgugaggcuugac
c

<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<....
..<<<<<<....(((.>>>.....<<<<<<<...<.))).....>.....
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......>
......>>>>>.>.........<<....>>...<<<<<.....<<.....
>>....>>>>>...(((........<<<<..<<<...<<<.<......>.
>>>((......<<<.....))>>>...>>>....>>>>............
........<<<<<<<<.........>>>>>>>>......<<<<<..<<<<
>>>>>..)))......]].>>>>>>>.]]...............<<....
>>....]].........<<<<.....>>>>............}....>>>
>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>...<.<..
......>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<.....>>
...>>>...<<....>>..<<<<<...>>>>>...>>>>>>>>>>>>>..
<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>
>>>>.....>>>...<<<.<<.<<........>>.>>>>>....>>>>>>
>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<...
.<<<<<....>>>>>.<<<<<<<<.....<<<<<<.....<<<...<<<.
<<<<...<..<<<.......>>>...>...>>>>.>>>..>>.>.....>
>>>>..>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>>..
..<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.....
......<<..<<<<<..<<........<<<<<..<...<<<.........
>>>...>.........<<<......>>>..>>>>>....>>..>>>>>.>
>...........)))...>>>>>>.>>>...>>>>>>><<<<<<......
>>>>>>....>>>>>><.<<<<<...<<<......<<<<<<<<....>>>
>>>>>...>>>..>>>>>..>.....>>>>>><......<<.....<<<<
<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<<<<...<<<...<<<....>>>...>>>...
>>>..<<<<<........>>>>>))<<<<<<<<<<<.<...<<<<....<
<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<....<<
<.<<<<<<<..<<.....>>.>>>>>>>...>>>....>>>...>><..<
<<<....>>>>...>>>>>>...>>>...>>>.>........>>>>...>
.....>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.
....>>>>..>>>>..<<<<....<<<<<<<<.<<...............
<<<<<....<<..>>.....>>>>><<<<<<..<<.....>>....>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<
<<........<<<<<<.<<....>>..>>>>>>........>>>>>>>>.
.>>>>><<<<<.........>>>>>........<...........<<<<<
.......>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>
>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<
<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<
<<<<.<<<<...........<<<<<...........<.<.<<<<....>>
>>.>.>..................>>>>>..>>>>.>>>>>>>>>>>...
<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<
.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<
<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<
<..<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<<<
<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>...
....<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.
......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<
<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>
>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<
<<<...............>>>>>>>.<<<<<...<<<...<<<<<<<<<<
.)))..>>>>>..>>>>>....>>>.>>>>>...<<<.<..<<<<<....
.......>>>>>...>>>>.>>>>.......>>>>>>>..<<<<<.....
>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<..<<...
..<<<......>>>....>>...>>>>>.>>>..>>>>.....>>>>>>>
.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6spd Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.
• Resolution: 3.28 Å
• Binding residue (original residue number in PDB): A11 G12 R13 R14 F15 K39 G42 R43 N44 N45 N46 R48 I49 T50 R52 K59 Q60 H61 Y62 R68 I74 Y83 R87 D98 R101 K147 K150 Q153 I154 A155 R156 S157 A158 L176 R177 S178 E180 R182 H200 S204 G206 K207 A208 G209 W213 R217 T219 R221 G222 V223 A224 M225 H230 G235 E236 G237 R238 S240 R243 P245 P248 W249 T253 K254 G255 T258 R259 K262 R263 R272
• Binding residue (residue number reindexed from 1): A9 G10 R11 R12 F13 K37 G40 R41 N42 N43 N44 R46 I47 T48 R50 K57 Q58 H59 Y60 R66 I72 Y81 R85 D96 R99 K145 K148 Q151 I152 A153 R154 S155 A156 L174 R175 S176 E178 R180 H198 S202 G204 K205 A206 G207 W211 R215 T217 R219 G220 V221 A222 M223 H228 G233 E234 G235 R236 S238 R241 P243 P246 W247 T251 K252 G253 T256 R257 K260 R261 R270

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6spd, PDBe:6spd, PDBj:6spd
• PDBsum: 6spd
• PubMed: 31611393
• UniProt: A0A241XHA2