Structure of PDB 4w2f Chain AI Binding Site BS01

Receptor Information

>4w2f Chain AI (length=127) Species: 300852 (Thermus thermophilus HB8)

EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLR
AVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGF
LTRDARVVERKKYGKHKARRAPQYSKR

Ligand information

>4w2f Chain AA (length=1497)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccugggaggcagcaguuaggaaucu
uccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagc
ccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggga
cugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcg
guaauacggagggcgcgagcguuacccggauucacugggcguaaagggcg
uguaggcggccuggggcgucccaugugaaagaccacggcucaaccguggg
ggagcgugggauacgcucaggcuagacggugggagagggugguggaauuc
ccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaa
ggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagc
aaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuag
gucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccug
gggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgca
caagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuacc
aggccuugacaugcuagggaacccgggugaaagccuggggugccccgcga
ggggagcccuagcacaggugcugcauggccgucgucagcucgugccguga
gguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugcca
gcgguucggccgggcacucuaacgggacugcccgcgaaagcgggaggaag
gaggggacgacgucuggucagcauggcccuuacggccugggcgacacacg
ugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcuaau
cgcaaaaaggugggcccaguucggauuggggucugcaacccgaccccaug
aagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauacgu
ucccgggccuuguacacaccgcccgucacgccaugggagcgggcucuacc
cgaagucgccgggagccuacgggcaggcgccgaggguagggcccgugacu
ggggcgaagucguaacaagguagcuguaccggaaggugcggcuggau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4w2f Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): Q3 Y5 T7 R9 K11 E12 R16 F18 R20 Y36 Q38 G39 Y62 G67 G68 G69 K70 S71 G72 Q73 R83 K97 T103 R104 A106 R107 V108 V109 E110 R111 K112 K113 Y114 G115 H117 K118 R120 R121 Q124 Y125 S126 R128
• Binding residue (residue number reindexed from 1): Q2 Y4 T6 R8 K10 E11 R15 F17 R19 Y35 Q37 G38 Y61 G66 G67 G68 K69 S70 G71 Q72 R82 K96 T102 R103 A105 R106 V107 V108 E109 R110 K111 K112 Y113 G114 H116 K117 R119 R120 Q123 Y124 S125 R127

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:4w2f, PDBe:4w2f, PDBj:4w2f
• PDBsum: 4w2f
• PubMed: 25306919
• UniProt: P80374|RS9_THET8 Small ribosomal subunit protein uS9 (Gene Name=rpsI)