Structure of PDB 4v95 Chain DR Binding Site BS01

Receptor Information

>4v95 Chain DR (length=118) Species: 300852 (Thermus thermophilus HB8)

MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDH
LIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKL
AERRRGDGAPLALVELVE

Ligand information

>4v95 Chain DA (length=2722)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucgcgaaucccca
gccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgu
aggcgaaagguggggggauaggugaggguacccgaguaccccgugguucg
uggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacucc
gggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacccc
gggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacg
gccccgcagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaaccgg
gcgagcuagcccuggccagggugaagcuggggugagacccaguggaggcc
cgaaccggugggggaugcaaaccccucggaugagcuggggcuaggaguga
aaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagg
gucagccucaggcgcugacuggggccuguagagcacugauagggcuaggg
ggcccaccagccuaccaaacccugucaaacuccgaagggucccaggugga
gccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaac
aaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaagga
uguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucuggggccccaggcgguaggggagcguucccgaug
ccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaau
gccggcaugaguaacgauaaagagggugagaaucccucucgccguaagcc
caaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaag
gugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccu
ucccgcaggugcgauggggggacgcucuaggcuagggggaccggagccau
ggacgagcccggccagaagcgcagggugggagguaggcaaauccgccucc
caacaagcucugcgugguggggaagcccgcgggugacaaccccccgaagc
cagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgc
aaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaac
ccucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggu
gcucccuggggugaugagccccggggagccgcagugaacaggcucuggcg
acuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauag
ggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagccc
cgaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggu
agcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacga
ccggagcgcugucucggcgagggacccggugaaauugaacuggccgugaa
gaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugc
agccugguguuggcucuuggucgcgcgcggcugggggccuaacccucgga
uggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaa
aagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgcc
ggagagcgcaaggguagaagggggccugacugcgaggccugcaagccgag
caggggcgaaagccgggccuagugaaccgguggucccguguggaagggcc
aucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccccc
gagcguccacagcggcggggagguuuggcaccucgaugucggcucgucgc
auccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaag
cggcacgcgagcuggguucagaacgucgugagacaguucggucucuaucc
gccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggacc
ggaagggacgcaccucugguuucccagcugucccuccaggggcauaagcu
ggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaag
cccgccccaagaugaggccucccacggcagccgguaaggacccgggaaga
ccacccgguggaugggccggggguguaagcgccgcgaggcguugagccga
ccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 H16 R17 N23 Q24 K26 S27 H31 I34 T36 T37 K40 K42 R45 G46 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 R77 R90 Q91 G92 G93 T95 R96 K99 R104 R105 G106 D107 V117
• Binding residue (residue number reindexed from 1): M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 H16 R17 N23 Q24 K26 S27 H31 I34 T36 T37 K40 K42 R45 G46 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 R77 R90 Q91 G92 G93 T95 R96 K99 R104 R105 G106 D107 V117

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v95, PDBe:4v95, PDBj:4v95
• PDBsum: 4v95
• PubMed: 22422986
• UniProt: Q9Z9H5|RL17_THET8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)