Structure of PDB 2qa4 Chain J Binding Site BS01

Receptor Information

>2qa4 Chain J (length=142) Species: 2238 (Haloarcula marismortui)

AEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQI
VEKYEKRVDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRV
YLGNPYDEDGEVLDGTSLDRLSNIKFVTLGEISETLGANKTW

Ligand information

>2qa4 Chain 0 (length=2753)

uaugccagcugguggauugcucggcucaggcgcugaugaaggacgugcca
agcugcgauaagccauggggagccgcacggaggcgaagaaccauggauuu
ccgaaugagaaucucuaacaauugcuucgcgcaaugaggaaccccgagaa
cugaaacaucucaguaucgggaggaacagaaaacgcaaugugaugucguu
aguaaccgcgagugaacgcgauacagcccaaaccgaagcccucacgggca
auguggugucagggcuaccucucaucagccgaccgucucgacgaagucuc
uuggaacagagcgugauacagggugacaaccccguacucgagaccaguac
gacgugcgguagugccagaguagcggggguuggauaucccucgcgaauaa
cgcaggcaucgacugcgaaggcuaaacacaaccugagaccgauagugaac
aaguagugugaacgaacgcugcaaaguacccucagaagggaggcgaaaua
gagcaugaaaucaguuggcgaucgagcgacagggcauacaaggucccucg
acgaaugaccgacgcgcgagcguccaguaagacucacgggaagccgaugu
ucugucguacguuuugaaaacgagccagggagugugucugcauggcaagu
cuaaccggaguauccggggaggcacagggaaaccgacauggccgcagggc
uugcccgagggccgccgucuucaagggcggggagccauguggacacgacc
cgaauccggacgaucuacgcauggacaagaugaagcgugccgaaaggcac
guggaagucuguuagaguugguguccuacaauacccucucgugaucuaug
uguaggggugaaaggcccaucgaguccggcaacagcugguuccaaucgaa
acaugucgaagcaugaccuccgccgagguagucugugagguagagcgacc
gauugguccugucaaacuccaaacuuacagacgccguuugacgcggggau
uccggugcgcgggguaagccuguguaccaggaggggaacaacccagagau
agguuaagguccccaaguguggauuaaguguaauccucugaagguggucu
cgagcccuagacagccgggaggugagcuuagaagcagcuacccucuaaga
aaagcguaacagcuuaccggccgagguuugaggcgcccaaaaugaucggg
acucaaauccaccaccgagaccuguccguaccacucauacugguaaucga
guagauuggcgcucuaauuggauggaaguaggggugaaaacuccuaugga
ccgauuagugacgaaaauccuggccauaguagcagcgauagucgggugag
aaccccgacggccuaauggauaaggguuccucagcacugcugaucagcug
aggguuagccgguccuaagucauaccgcaacucgacuaugacgaaauggg
aaacggguuaauauucccgugccacuaugcagugaaaguugacgcccugg
ggucgaucacgcugggcaucgcccagucgaaccguccaacuccguggaag
ccguaauggcaggaagcggacgaacggcggcauagggaaacgugauucaa
ccuggggcccaugaaaagacgagcauaguguccguaccgagaaccgacac
agguguccauggcggcgaaagccaaggccugucgggagcaaccaacguua
gggaauucggcaaguuagucccguaccuucggaagaagggaugccugcuc
cggaacggagcaggucgcagugacucggaagcucggacugucuaguaaca
acauaggugaccgcaaauccgcaaggacucguacggucacugaauccugc
ccagugcagguaucugaacaccucguacaagaggacgaaggaccugucaa
cggcgggggucuuaagguagcguaguaccuugccgcaucaguagcggcuu
gcaugaauggauuaaccagagcuucacugucccaacguugggcccgguga
acuguacauuccagugcggagucuggagacacccagggggaagcgaagac
ccuauggagcuuuacugcaggcugucgcugaggacucucacuccgggagg
aggacaccgauagccgggcaguuugacuggggcgguacgcgcucgaaaag
auaucgagcgcgcccuauggcuaucucagccggggacccggcgaagagug
caagagcaaaagauagcuugacaguguucuucccaacgaggaacgcugac
gcgaaagcguggucuagcgaaccaauuagccugcuugaugcgggcaauug
augacagaaaagcuacccuagggauaacagagucgucacucgcaagagca
cauaucgaccgaguggcuugcuaccucgaugucgguucccuccauccugc
ccgugcagaagcgggcaagggugagguuguucgccuauuaaaggaggucg
ugagcuggguuuagaccgucgugagacaggucggcugcuaucuacugggu
guguaggugucugacaagaacgaccguauaguacgagaggaacuacgguu
gguggccacugguguaccgguuguucgagagagcacgugccggguagcca
cgccacacgggguaagagcugaacgcaucuaagcucgaaacccacuugga
aaagagacaccgccgaggucccgcguacaagacgcggucgauagacucgg
ggugugcgcgucgagguaacgagacguuaagcccacgagcacuaacagac
caa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2qa4 Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: Analysis of L11 movements
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): I18 G20 R21 S24 T47 R49 Q52 K59 R60 I63 N65 N67 G68 Y69 F70 P72 K73 R74 K80 R81 T82 R84 G85 M86 H89 K90 K91 R95 R102 V103 Y104 I127 K128 G140
• Binding residue (residue number reindexed from 1): I15 G17 R18 S21 T44 R46 Q49 K56 R57 I60 N62 N64 G65 Y66 F67 P69 K70 R71 K77 R78 T79 R81 G82 M83 H86 K87 K88 R92 R99 V100 Y101 I124 K125 G137

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of 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:2qa4, PDBe:2qa4, PDBj:2qa4
• PDBsum: 2qa4
• PubMed: 17599351
• UniProt: P29198|RL13_HALMA Large ribosomal subunit protein uL13 (Gene Name=rpl13)