Structure of PDB 5ndk Chain 78 Binding Site BS01

Receptor Information

>5ndk Chain 78 (length=147) Species: 300852 (Thermus thermophilus HB8)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVL

Ligand information

>5ndk Chain 1H (length=2912)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccga
aaaguccgcggccguggacccgaaaccgggcgagcuagcccuggccaggg
ugaagcuggggugagacccaguggaggcccgaaccggugggggaugcaaa
ccccucggaugagcuggggcuaggagugaaaagcuaaccgagcccggaga
uagcugguucuccccgaaaugacuuuagggucagccucaggcgcugacug
gggccuguagagcacugauagggcuagggggcccaccagccuaccaaacc
cugucaaacuccgaagggucccagguggagccugggagugagggcgcgag
cgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaagg
cccccaagucugggcuaagugguaaaggauguggcgccgcgaagacagcc
aggauguuggcuuagaagcagccaucauuuaaagagugcguaauagcuca
cuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgcc
gaagcugcgggucugggggaugaccccaggcgguaggggagcguucccga
ugccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcga
augccggcaugaguaacgauaaagagggugagaaucccucucgccguaag
cccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccua
aggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcc
cuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagcc
auggacgagcccggccagaagcgcagggugggagguaggcaaauccgccu
cccaacaagcucugcgugguggggaagcccguacgggugacaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndk Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): L3 S4 R7 P8 N9 G11 A12 N13 K14 R15 R16 K17 R18 V19 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 L45 K46 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 G69 Q70 V71 P72 G73 E74 I75 R77 Q81 N84 R90 G104 K107 K108 K113 L115 G116 E117 S131 K132 S133
• Binding residue (residue number reindexed from 1): L3 S4 R7 P8 N9 G11 A12 N13 K14 R15 R16 K17 R18 V19 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 L45 K46 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 G69 Q70 V71 P72 G73 E74 I75 R77 Q81 N84 R90 G104 K107 K108 K113 L115 G116 E117 S131 K132 S133

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:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndk, PDBe:5ndk, PDBj:5ndk
• PDBsum: 5ndk
• PubMed: 29208708
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)