Structure of PDB 5ndj Chain C5 Binding Site BS01

Receptor Information
>5ndj Chain C5 (length=104) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRV
SPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAK
CGGA
Ligand information
>5ndj Chain 14 (length=2909) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaa
guccgcggccguggacccgaaaccgggcgagcuagcccuggccaggguga
agcuggggugagacccaguggaggcccgaaccggugggggaugcaaaccc
cucggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauag
cugguucuccccgaaaugacuuuagggucagccucaggcgcugacugggg
ccuguagagcacugauagggcuagggggcccaccagccuaccaaacccug
ucaaacuccgaagggucccagguggagccugggagugagggcgcgagcga
uaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccc
ccaagucugggcuaagugguaaaggauguggcgccgcgaagacagccagg
auguuggcuuagaagcagccaucauuuaaagagugcguaauagcucacug
gucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaa
gcugcgggucugggggaugaccccaggcgguaggggagcguucccgaugc
cgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaug
ccggcaugaguaacgauaaagagggugagaaucccucucgccguaagccc
aaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagg
ugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuu
cccgcaggugcgauggggggacgcucuaggcuagggggaccggagccaug
gacgagcccggccagaagcgcagggugggagguaggcaaauccgccuccc
aacaagcucugcgugguggggaagcccguacgggugacaaccccccgaag
ccagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccg
caaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaa
cccucgccaaggaacucugcaaguuggccccguaacuucgggagaagggg
ugcucccuggggugaugagccccggggagccgcagugaacaggcucuggc
gacuguuuaccaaaaacacagcucucugcgaacucguaagaggagguaua
gggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcc
ccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacg
accggagcgcugucucggcgagggacccggugaaauugaacuggccguga
agaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacug
cagccugguguuggcucuuggucgcgccugcguaggauaggugggagccu
gugaacccccgccuccgggugggggggaggcgccggugaaauaccacccu
ggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggc
aguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagg
uccccucaggcgggacggaaauccgccggagagcgcaaggguagaagggg
gccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagu
gaaccgguggucccguguggaagggccaucgaucaacggauaaaaguuac
cccggggauaacaggcugaucucccccgagcguccacagcggcggggagg
uuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccc
aaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaa
cgucgugagacaguucggucucuauccgccacgggcgcaggaggcuugag
gggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuc
ccagcugucccuccaggggcauaagcuggguagccaugugcggaagggau
aaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccc
acggcgucaagccgguaaggacccgggaagaccacccgguggaugggccg
gggguguaagcgccgcgaggcguugagccgaccggucccaaucguccgag
gucuugacc
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<<<<<..>>>>>>.>>....<<<<<.....<......>......>>>>>.
..........<<....>>...<<<<<.....<<.....>>....>>>>>.
..<<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<.....<
<<...<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.
....))>>>...>>>...>>>>..>>>>>..>>>.>>>>>.>>>.....<
<<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>
>......>>.>>>>>>.>>...............<<....>>....>>..
.......<<<<....>>>>..................>>>>>>>>>>>..
.....<<<<<<<<<<<....>>>>>>>>>>>...<............>.<
<<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...
<<....>>..<<<<.....>>>>.....<<<<..........>>>>....
>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<......>>>>>>.....>>>...<<<<.<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<
<<<...<<<...<<<<<<<<...<<.<<........>>..>>...>>>>>
>>>..>>.>...>>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<..
....>>.>>>>>>>.....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<<<<<......<.<<<<<.
<<.....................>>.........<........>...>>>
>>.>..>>>>>>>>>.>>..........)))......>>>>>>.>>>...
>>>>>>><<<<<<<<.....>>>>>>>>....>>>>>>..<<<<<...<<
<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>........>
>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<
<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<
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<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[
[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>
.....>>>>>>>>>..>>><...<<<<....>>>>.....>>>>>>...>
>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>>.
....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....
<<<<<<<<.<<.........<.....<<<<<.....<..>......>>>>
><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<<<
<..<<<.........>>>..<<<<<<<.....<<<....>>>.......>
>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>
>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<<.....>>>>>>.....>....>>>>>..>>
.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<...
.....>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<<<
<.<<<.<<<<<.<<<<<<<<<<<<<<<<...........<<.......<.
.......<<<<<<<..>>>>>>>.....>.................>>..
>>>>>>>>>>>>>>>>...<<<<<....>>>>>....>>>>>.>>>..>>
>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...<<
<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>>>
>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))...
....<<<<<<<.<<..))))..>>>>>>>>>.............>>>>..
>>>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>>.
...>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>
..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<
<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<<<...<
<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<...
<<<<<<<<<<<]]]]>>>>>>...>>>>>...>>>>.>>>>>...<<<..
..<<<<<...........>>>>>....>>>.>>>>.......>>>>>>>.
...<.......>......<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ndj Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		R2 H6 K8 K9 S17 G18 K19 V30 P32 Y35 I44 V45 K46 K47 A48 V49 K54 F60 H68 S70 K71 R73 K81 T83 V85
Binding residue
(residue number reindexed from 1)		R1 H5 K7 K8 S16 G17 K18 V29 P31 Y34 I43 V44 K45 K46 A47 V48 K53 F59 H67 S69 K70 R72 K80 T82 V84
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ndj, PDBe:5ndj, PDBj:5ndj
PDBsum5ndj
PubMed29208708
UniProtQ5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)

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