Structure of PDB 3g4s Chain E Binding Site BS01

Receptor Information

>3g4s Chain E (length=172) Species: 2238 (Haloarcula marismortui)

PRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIE
SDEDNAKTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGD
EVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQ
LTRINDKDVRVFQDGVYITRKP

Ligand information

>3g4s Chain 0 (length=2754)

uaugccagcugguggauugcucggcucaggcgcugaugaaggacgugcca
agcugcgauaagcuguggggagccgcacggaggcgaagaaccacagauuu
ccgaaugagaaucucuaacaauugcuucgcgcaaugaggaaccccgagaa
cugaaacaucucaguaucgggaggaacagaaaacgcaacgugaugucguu
aguaaccgcgagugaacgcgauacagcccaaaccgaagcccucacgggca
auguggugucagggcuaccucucaucagccgaccgucuucacgaagucuc
uuggaauagagcgugauacagggugacaaccccguacugaagaccaguac
gcugugcgguagugccagaguagcggggguuggauaucccucgcgaauaa
cgcaggcaucgacugcgaaggcuaaacacaaccugagaccgauagugaac
aaguagugugaacgaacgcugcaaaguacccucagaagggaggcgaaaua
gagcaugaaaucaguuggcgaucgagcgacagggcauacaaggucccuug
acgaaugaccgagacgcgagucuccaguaagacucacgggaagccgaugu
ucugucguacguuuugaaaaacgagccagggagugugucuguauggcaag
ucuaaccggaguauccggggaggcacagggaaaccgacauggccgcaggg
cuugcccgagggccgccgucuucaagggcggggagccauguggacacgac
ccgaauccggacgaucuacgcauggacaagaugaagcgugccgaaaggca
cguggaagucuguuagaguugguguccuacaauacccucucgugaucuau
guguaggggugaaaggcccaucgaguccggcaacagcugguuccaaucga
aacaugucgaagcaugaccuccgccgagguagucugugagguagagcgac
cgauugguccugucaaacuccaaacuuacagacgcuguuugacgcgggga
uuccggugcgcgggguaagccuguguaccaggaggggaacaacccagaga
uagguuaagguccccaaguguggauuaaguguaauccucugaaggugguc
ucgagcccuagacagccgggaggugagcuuagaagcagcuacccucuaag
aaaagcguaacagcuuaccggccgagguuugaggcgcccaaaaugaucgg
gacucaaauccaccaccgagaccuguccguaccacucauacugguaaucg
aguagauuggcgcucuaauuggauggaagcaggggcgagagcuccugugg
accgauuagugacgaaaauccuggccauaguagcagcgauagucggguga
gaaccccgacggccuaauggauaaggguuccucagcacugcugaucagcu
gaggguuagccgguccuaagucucaccgcaacucgacugagacgaaaugg
gaaacagguuaauauuccugugccaucaugcagugaaaguugacgcccug
gggucgaucacgccgggcaucgcccggucgaaccguccaacuccguggaa
gccguaauggcaggaagcggacgaacggcggcauagggaaacgugauuca
accuggggcccaugaaaagacgagcaugauguccguaccgagaaccgaca
cagguguccauggcggcgaaagccaaggccugucgggagcaaccaacguu
agggaauucggcaaguuagucccguaccuucggaagaagggaugccugcu
ccggaacggagcaggucgcagugacucggaagcucggacugucuaguaac
aacauaggugaccgcaaauccgcaaggacucguacggucacugaauccug
cccagugcagguaucugaacaccucguacaagaggacgaaggaccuguca
acggcgggggucuuaagguagcguaguaccuugccgcaucaguagcggcu
ugcaugaauggauuaaccagagcuucacugucccaacguugggcccggug
aacuguacauuccagugcggagucuggagacacccagggggaagcgaaga
cccuauggagcuuuacugcaggcugucgcugaggacucucacuccgggag
gaggacaccgauagccgggcaguuugacuggggcgguacgcgcucgaaaa
gauaucgagcgcgcccuauggucaucucagccggggacccggcgaagagu
gcaagagcaaaagaugacuugacaguguucuucccaacgaggaacgcuga
cgcgaaagcguggucuagcgaaccaauuagccugcuugaugcgggcaauu
gaugacagaaaagcuacccuagggauaacagagucgucacucgcaagagc
acauaucgaccgaguggcuugcuaccucgaugucgguucccuccauccug
cccgugcagaagcgggcaagggugagguuguucgccuauuaaaggagguc
gugagcuggguuuagaccgucgugagacaggucggcugcuaucuacuggg
uguguaggugucugacaagaacgaccguauaguacgagaggaacuacggu
ugguggccacugguguaccgguuguucgagagagcacgugccggguagcc
acgccacacgggguaagagcugaacgcaucuaagcucgaaacccacuugg
aaaagagacaccgccgaggucccgcguacaagacgcggucgauagacucg
gggugugcgcgucgagguaacgagacguuaagcccacgagcacuaacaga
ccaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3g4s U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): Y35 A56 S60 G63 T64 S67 H68 Y82 H90 F91 L108 G109 E110 K111 A112 H119 I138 E139 G142 Q143 A146 Q150 R153 N155 K157 D158 R160 V161 F162
• Binding residue (residue number reindexed from 1): Y35 A56 S60 G63 T64 S67 H68 Y82 H90 F91 L108 G109 E110 K111 A112 H119 I138 E139 G142 Q143 A146 Q150 R153 N155 K157 D158 R160 V161 F162

Gene Ontology

Molecular Function

• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3g4s, PDBe:3g4s, PDBj:3g4s
• PDBsum: 3g4s
• PubMed: 19362093
• UniProt: P14135|RL6_HALMA Large ribosomal subunit protein uL6 (Gene Name=rpl6)