Structure of PDB 6spd Chain N Binding Site BS01

Receptor Information
>6spd Chain N (length=118) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRHRKSGRHLSRTSAHRKAMFQNMAVSLFEHELIKTTLPKAKELRRVAEP
LITLAKEDSVANRRLAFDRTRSKAAVGKLFNDLGKRYANRPGGYLRILKC
GFRAGDNAPMAYVELVDR
Ligand information
>6spd Chain A (length=2851) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<....
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<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......>
......>>>>>.>.........<<....>>...<<<<<.....<<.....
>>....>>>>>...(((........<<<<..<<<...<<<.<......>.
>>>((......<<<.....))>>>...>>>....>>>>............
........<<<<<<<<.........>>>>>>>>......<<<<<..<<<<
>>>>>..)))......]].>>>>>>>.]]...............<<....
>>....]].........<<<<.....>>>>............}....>>>
>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>...<.<..
......>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<.....>>
...>>>...<<....>>..<<<<<...>>>>>...>>>>>>>>>>>>>..
<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>
>>>>.....>>>...<<<.<<.<<........>>.>>>>>....>>>>>>
>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<...
.<<<<<....>>>>>.<<<<<<<<.....<<<<<<.....<<<...<<<.
<<<<...<..<<<.......>>>...>...>>>>.>>>..>>.>.....>
>>>>..>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>>..
..<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.....
......<<..<<<<<..<<........<<<<<..<...<<<.........
>>>...>.........<<<......>>>..>>>>>....>>..>>>>>.>
>...........)))...>>>>>>.>>>...>>>>>>><<<<<<......
>>>>>>....>>>>>><.<<<<<...<<<......<<<<<<<<....>>>
>>>>>...>>>..>>>>>..>.....>>>>>><......<<.....<<<<
<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<<<<...<<<...<<<....>>>...>>>...
>>>..<<<<<........>>>>>))<<<<<<<<<<<.<...<<<<....<
<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<....<<
<.<<<<<<<..<<.....>>.>>>>>>>...>>>....>>>...>><..<
<<<....>>>>...>>>>>>...>>>...>>>.>........>>>>...>
.....>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.
....>>>>..>>>>..<<<<....<<<<<<<<.<<...............
<<<<<....<<..>>.....>>>>><<<<<<..<<.....>>....>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<
<<........<<<<<<.<<....>>..>>>>>>........>>>>>>>>.
.>>>>><<<<<.........>>>>>........<...........<<<<<
.......>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>
>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<
<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<
<<<<.<<<<...........<<<<<...........<.<.<<<<....>>
>>.>.>..................>>>>>..>>>>.>>>>>>>>>>>...
<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<
.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<
<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<
<..<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<<<
<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>...
....<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.
......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<
<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>
>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<
<<<...............>>>>>>>.<<<<<...<<<...<<<<<<<<<<
.)))..>>>>>..>>>>>....>>>.>>>>>...<<<.<..<<<<<....
.......>>>>>...>>>>.>>>>.......>>>>>>>..<<<<<.....
>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<..<<...
..<<<......>>>....>>...>>>>>.>>>..>>>>.....>>>>>>>
.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6spd Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.
Resolution3.28 Å
Binding residue
(original residue number in PDB)
M1 R2 H3 R4 K5 S6 R8 H9 S11 R12 H16 K18 N23 P39 K40 K42 R45 R46 T53 R63 R64 D68 R71 K73 R90 G92 G93 L95 R96 K99 D106 N107 A108
Binding residue
(residue number reindexed from 1)
M1 R2 H3 R4 K5 S6 R8 H9 S11 R12 H16 K18 N23 P39 K40 K42 R45 R46 T53 R63 R64 D68 R71 K73 R90 G92 G93 L95 R96 K99 D106 N107 A108
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6spd, PDBe:6spd, PDBj:6spd
PDBsum6spd
PubMed31611393
UniProtA0A072ZCA1

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