Structure of PDB 1w2b Chain E Binding Site BS01

Receptor Information

>1w2b Chain E (length=172) Species: 2238 (Haloarcula marismortui)

PRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIE
SDEDNAKTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGD
EVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQ
LTRINDKDVRVFQDGVYITRKP

Ligand information

>1w2b Chain 0 (length=2754)

uaugccagcugguggauugcucggcucaggcgcugaugaaggacgugcca
agcugcgauaagccauggggagccgcacggaggcgaagaaccauggauuu
ccgaaugagaaucucuaacaauugcuucgcgcaaugaggaaccccgagaa
cugaaacaucucaguaucgggaggaacagaaaacgcaaugugaugucguu
aguaaccgcgagugaacgcgauacagcccaaaccgaagcccucacgggca
auguggugucagggcuaccucucaucagccgaccgucucgacgaagucuc
uuggaacagagcgugauacagggugacaaccccguacucgagaccaguac
gacgugcgguagugccagaguagcggggguuggauaucccucgcgaauaa
cgcaggcaucgacugcgaaggcuaaacacaaccugagaccgauagugaac
aaguagugugaacgaacgcugcaaaguacccucagaagggaggcgaaaua
gagcaugaaaucaguuggcgaucgagcgacagggcauacaaggucccucg
acgaaugaccgacgcgcgagcguccaguaagacucacgggaagccgaugu
ucugucguacguuuugaaaaacgagccagggagugugucugcauggcaag
ucuaaccggaguauccggggaggcacagggaaaccgacauggccgcaggg
cuugcccgagggccgccgucuucaagggcggggagccauguggacacgac
ccgaauccggacgaucuacgcauggacaagaugaagcgugccgaaaggca
cguggaagucuguuagaguugguguccuacaauacccucucgugaucuau
guguaggggugaaaggcccaucgaguccggcaacagcugguuccaaucga
aacaugucgaagcaugaccuccgccgagguagucugugagguagagcgac
cgauugguccugucaaacuccaaacuuacagacgccguuugacgcgggga
uuccggugcgcgggguaagccuguguaccaggaggggaacaacccagaga
uagguuaagguccccaaguguggauuaaguguaauccucugaaggugguc
ucgagcccuagacagccgggaggugagcuuagaagcagcuacccucuaag
aaaagcguaacagcuuaccggccgagguuugaggcgcccaaaaugaucgg
gacucaaauccaccaccgagaccuguccguaccacucauacugguaaucg
aguagauuggcgcucuaauuggauggaaguaggggugaaaacuccuaugg
accgauuagugacgaaaauccuggccauaguagcagcgauagucggguga
gaaccccgacggccuaauggauaaggguuccucagcacugcugaucagcu
gaggguuagccgguccuaagucauaccgcaacucgacuaugacgaaaugg
gaaacggguuaauauucccgugccacuaugcagugaaaguugacgcccug
gggucgaucacgcugggcaucgcccagucgaaccguccaacuccguggaa
gccguaauggcaggaagcggacgaacggcggcauagggaaacgugauuca
accuggggcccaugaaaagacgagcauaguguccguaccgagaaccgaca
cagguguccauggcggcgaaagccaaggccugucgggagcaaccaacguu
agggaauucggcaaguuagucccguaccuucggaagaagggaugccugcu
ccggaacggagcaggucgcagugacucggaagcucggacugucuaguaac
aacauaggugaccgcaaauccgcaaggacucguacggucacugaauccug
cccagugcagguaucugaacaccucguacaagaggacgaaggaccuguca
acggcgggggucuuaagguagcguaguaccuugccgcaucaguagcggcu
ugcaugaauggauuaaccagagcuucacugucccaacguugggcccggug
aacuguacauuccagugcggagucuggagacacccagggggaagcgaaga
cccuauggagcuuuacugcaggcugucgcugaggacucucacuccgggag
gaggacaccgauagccgggcaguuugacuggggcgguacgcgcucgaaaa
gauaucgagcgcgcccuauggcuaucucagccggggacccggcgaagagu
gcaagagcaaaagauagcuugacaguguucuucccaacgaggaacgcuga
cgcgaaagcguggucuagcgaaccaauuagccugcuugaugcgggcaauu
gaugacagaaaagcuacccuagggauaacagagucgucacucgcaagagc
acauaucgaccgaguggcuugcuaccucgaugucgguucccuccauccug
cccgugcagaagcgggcaagggugagguuguucgccuauuaaaggagguc
gugagcuggguuuagaccgucgugagacaggucggcugcuaucuacuggg
uguguaggugucugacaagaacgaccguauaguacgagaggaacuacggu
ugguggccacugguguaccgguuguucgagagagcacgugccggguagcc
acgccacacgggguaagagcugaacgcaucuaagcucgaaacccacuugg
aaaagagacaccgccgaggucccgcguacaagacgcggucgauagacucg
gggugugcgcgucgagguaacgagacguuaagcccacgagcacuaacaga
ccaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1w2b Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): N55 A56 S60 T64 S67 H68 N71 Y82 H90 F91 G109 E110 K111 A112 I138 E139 Q143 A146 Q150 R153 K157 D158 V161 F162
• Binding residue (residue number reindexed from 1): N55 A56 S60 T64 S67 H68 N71 Y82 H90 F91 G109 E110 K111 A112 I138 E139 Q143 A146 Q150 R153 K157 D158 V161 F162
• Binding affinity: PDBbind-CN: Kd=1.2uM

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:1w2b, PDBe:1w2b, PDBj:1w2b
• PDBsum: 1w2b
• PubMed: 15334087
• UniProt: P14135|RL6_HALMA Large ribosomal subunit protein uL6 (Gene Name=rpl6)