Structure of PDB 6d9j Chain MM Binding Site BS01

Receptor Information
>6d9j Chain MM (length=143) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIQTERAYQKQPTIFQNKKRVKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMS
VHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKK
Ligand information
>6d9j Chain 2 (length=1697) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgacuuggauaacugugguaau
ucuagagcuaauacaugccgacgggcgcugacccccuucgcgggggggau
gcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacgc
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucuugggagcggccguccccugcucggcgccggcccgaagc
guuuacuuugaaaaaauuagaguguucaaagcaggccgccuggauaccgc
agcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuucgga
acugaggccaugauuaagagggacggccgggggcauucguauugcgccgc
uagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagcauu
ugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaagac
gaucagauaccgucguaguuccgaccauaaacgaugccgaccggcgaugc
ggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaaguc
uuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaauug
acggaagggcaccaccaggaguggagccugcggcuuaauuugacucaaca
cgggaaaccucacccggcccggacacggacaggauugacagauugauagc
ucuuucucgauuccgugggugguggugcauggccguucuuaguuggugga
gcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcuaac
uaguuacgcgaccccggucggcguaacuucuuagagggacaaguggcguu
cagccacccgagauugagcaauaacaggucugugaugcccuuagaugucc
ggggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacg
ccggcaggcgcggguaacccguugaaccccauucgugauggggaucgggg
auugcaauuauuccccaugaacgaggaauucccaguaagugcgggucaua
agcuugcguugauuaagucccugcccuuuguacacaccgcccgucgcuac
uaccgauuggaugguuuagugaggcccucggaucggccccgccggggugc
ccuggcggagcgcugagaagacggucgaacuugacuaucuagaggaagua
aaagucguaacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<.........<<<.
<<<...<....<<....<<..........>>...>>.>.......<<...
.....<<<.......<....<<<<<........<<.....<<..<.....
..>..>>......>>.........<<<<...<<<<<<....>>>>.>>..
>>>><<..<<<<<.............>>>>>......>>...<<<..<<<
<.>>>>.>>>.>>.>>>....>....>>>.<<<....<<<....<<<<<<
<.........>>>>>>>>>>......>>>...<<<.<<<<....>>>>..
..>>>.>>.<<.<<<..........>>>.>>...<<....>>.....>>>
>>>.........<<<....<<<.....>>>..>>>......>>.>.....
<<<<<<.<<.<<<....>>>..>>.>>>.>>>......<<..<.......
....>..>>.........<<<<<((......<<<<.....<<..))>>..
.....>>>>.>>>>>..>>>>>>.>>>...........<((.....<.<<
...<<<.<<....<<<.<<<..>>>.>>>.<<<<<<.<<..>>>>>>.>>
..<<<.<<.<.......<<...<.......>.<<<<.>>>>...>>....
..>.>>...>>>........<.<<.<<<<<<<...............>>>
>>>>.>>.>....>>....<<<<<<......<<<<..<<<.<<<<<<<<.
..<<<......>>>......>>>>>>>>.>>>.......<<....>>...
>>>>.....>>>.>>>...>>>...>>.>....<<<<<<<...<...<<<
<.........>>>>...>>>>>>>>..........<<<.<<.<<<..<.<
<<<<<.<<<<......>>>>>>>>>>.>..>>>...<<..))>>...>>.
....>>>.>....<<......<<<......>>>....>>...)))).]..
<<<.<<<<<<<..<<..<<<<<..<<<.<<<<<<......<<........
>>..........<<<<<.<....<<<<<<.......<<.<<<........
>>>.>>.....>>>>>>...<<.<<<..<<.<<<<<<....<<<.<<<..
......>...<<<......>>>...>>.>>>....<<<...<...<<<<.
.<<<<<<<<<<<<..>>>>.>>>>>>>>..>>>>..>.....<<<<<...
..>>>>>........>>>....>>>.>>>.....>>>>>>>.....>.>>
>>>...>>.>>>>.>>>.....<<.<<<........<.......<<<..<
<<....>>>..>>>....>.........>>>.>>......<.....<<<<
<..........>>>>>.....>.....>>>>>.....<<<<<<<<.....
..>>>>>>>>......>>...>>>>>>>>>>..........<<.<..<<<
<.<<....<<<<<<<<.<<<...<<<.<<...<<<<<.<<<<<<<<....
>>>>>>>>...>>>>>...>>.>>>...>>>.>>>>>>>>...>>.>>>>
...>.>>.........<<<<<<<<<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6d9j Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		E7 Q11 T15 F17 Y36 N39 I40 G41 L42 K58 K59 G64 S67 R69 R71 M82 R89 Y92 H94 R97 K98 Y99 K104 R105 H106 K107 N108 E130 R132 P133 S135 K136 T137 A149
Binding residue
(residue number reindexed from 1)		E5 Q9 T13 F15 Y26 N29 I30 G31 L32 K48 K49 G54 S57 R59 R61 M72 R79 Y82 H84 R87 K88 Y89 K94 R95 H96 K97 N98 E120 R122 P123 S125 K126 T127 A139
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small 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:6d9j, PDBe:6d9j, PDBj:6d9j
PDBsum6d9j
PubMed29856316
UniProtG1TRM4|RS11_RABIT Small ribosomal subunit protein uS17 (Gene Name=RPS11)

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