Structure of PDB 1vy6 Chain CI Binding Site BS01

Receptor Information

>1vy6 Chain CI (length=127) Species: 300852 (Thermus thermophilus HB8)

EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLR
AVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGF
LTRDARVVERKKYGKHKARRAPQYSKR

Ligand information

>1vy6 Chain CA (length=1503)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcgggguacuccguggucagcggcggacggg
ugaguaacgcgugggugaccuacccggaagagggggacaacccggggaaa
cucgggcuaaucccccauguggacccgccccuugggguguguccaaaggg
cuuugcccgcuuccggaugggcccgcgucccaucagcuaguugguggggu
aauggcccaccaaggcgacgacggguagccggucugagaggauggccggc
cacaggggcacugagacacgggccccacuccuacgggaggcagcaguuag
gaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggagga
agaagcccuucgggguguaaacuccugaacccgggacgaaacccccgacg
aggggacugacgguaccgggguaauagcgccggccaacuccgugccagca
gccgcgguaauacggagggcgcgagcguuacccggauucacugggcguaa
agggcguguaggcggccuggggcgucccaugugaaagaccacggcucaac
cgugggggagcgugggauacgcucaggcuagacggugggagaggguggug
gaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccgau
ggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcgug
gggagcaaaccggauuagauacccggguaguccacgcccuaaacgaugcg
cgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgcgc
cgccuggggaguacggccgcaaggcugaaacucaaaggaauugacggggg
cccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaac
cuuaccaggccuugacaugcuagggaacccgggugaaagccuggggugcc
ccgcgaggggagcccuagcacaggugcugcauggccgucgucagcucgug
ccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguuag
uugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcggg
aggaaggaggggacgacgucuggucagcauggcccuuacggccugggcga
cacacgugcuacaaugcccacuacaaagcgaugccacccggcaacgggga
gcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccgac
cccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcgguga
auacguucccgggccuuguacacaccgcccgucacgccaugggagcgggc
ucuacccgaagucgccgggagccuacgggcaggcgccgaggguagggccc
gugacuggggcgaagucguaacaagguagcuguaccggaaggugcggcug
gau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1vy6 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): Q3 Y5 R9 E12 R16 F18 R20 Y36 Q38 R66 G67 G68 G69 K70 G72 Q73 R83 R93 T103 R104 R107 V108 V109 E110 R111 K112 K113 Y114 G115 H117 A119 R120 R121 A122 Q124 Y125 S126
• Binding residue (residue number reindexed from 1): Q2 Y4 R8 E11 R15 F17 R19 Y35 Q37 R65 G66 G67 G68 K69 G71 Q72 R82 R92 T102 R103 R106 V107 V108 E109 R110 K111 K112 Y113 G114 H116 A118 R119 R120 A121 Q123 Y124 S125

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1vy6, PDBe:1vy6, PDBj:1vy6
• PDBsum: 1vy6
• PubMed: 25132179
• UniProt: P80374|RS9_THET8 Small ribosomal subunit protein uS9 (Gene Name=rpsI)