Structure of PDB 2qa4 Chain M Binding Site BS01

Receptor Information

>2qa4 Chain M (length=194) Species: 2238 (Haloarcula marismortui)

ARSAYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKAR
SQGYKAKQGVIVARVSVRKGSARKRRHKAGRRSKRQGVTRITRRKDIQRV
AEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPAIQNDDDLSWI
CADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSNGGKA

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): A1 S3 Y5 R9 E13 P15 W25 Q29 R32 A36 R39 R42 R45 L46 K48 R50 S51 Q52 A56 Q58 R68 S71 R73 R75 R76 A79 G80 R81 R82 S83 K84 R85 Q86 R90 I91 T92 R93 R94 K95 D96 I97 R99 V100 R104 R107 F109 P110 N111 N116 G124 R125 K127 D135 N137 H138 P139 D146 W149 A156 D157 R161 L163 R168 N170 R171 G172 K176 K178 G179 E181 K182 R184 P185 S186 R188 G191 K193 A194
• Binding residue (residue number reindexed from 1): A1 S3 Y5 R9 E13 P15 W25 Q29 R32 A36 R39 R42 R45 L46 K48 R50 S51 Q52 A56 Q58 R68 S71 R73 R75 R76 A79 G80 R81 R82 S83 K84 R85 Q86 R90 I91 T92 R93 R94 K95 D96 I97 R99 V100 R104 R107 F109 P110 N111 N116 G124 R125 K127 D135 N137 H138 P139 D146 W149 A156 D157 R161 L163 R168 N170 R171 G172 K176 K178 G179 E181 K182 R184 P185 S186 R188 G191 K193 A194

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:2qa4, PDBe:2qa4, PDBj:2qa4
• PDBsum: 2qa4
• PubMed: 17599351
• UniProt: P60618|RL15E_HALMA Large ribosomal subunit protein eL15 (Gene Name=rpl15e)