Structure of PDB 7v2o Chain D Binding Site BS01

Receptor Information

>7v2o Chain D (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

Ligand information

>7v2o Chain A (length=1487)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcgggguuuuacuccguggucagcggcggac
gggugaguaacgcgugggugaccuacccggaagagggggacaacccgggg
aaacucgggcuaaucccccauguggacccgccccuugggguguguccaaa
gggcuuugcccgcuuccggaugggcccgcgucccaucagcuaguuggugg
gguaauggcccaccaaggcgacgacggguagccggucugagaggauggcc
ggccacaggggcacugagacacgggccccacuccuacgggaggcagcagu
uaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuugga
ggaagaagcccuucgggguguaaacuccugaacccgggacgaaacccccg
acgaggggacugacgguaccgggguaauagcgccggccaacuccgugcca
gcagccgcgguaauacggagggcgcgagcguuacccggauucacugggcg
uaaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuc
aaccgugggggagcgugggauacgcucaggcuagacggugggagagggug
guggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgcc
gauggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagc
guggggagcaaaccggauuacccggguaguccacgcccuaaacgaugcgc
gcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgcgcc
gccuggggaguacggccgcaaggcugaaacucaaaggaauugacgggggc
ccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaacc
uuaccaggccuugacaugcuagggaacccgggugaaagccuggggugccc
cgcgaggggagcccuagcacaggugcugcauggccgucgucagcucgugc
cgugagguguuggguuaagucccgcaacgagcgcaacccccgccguuagu
ugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcggga
ggaaggaggggacgacgucuggucagcauggcccuuacggccugggcgac
acacgugcuacaaugcccacuacaaagcgaugccacccggcaacggggag
cuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccgacc
ccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaa
uacguucccgggccuuguacaccgucacgccaugggagcgggcucuaccc
gaagucgccgggagccuacgggcaggcgccgaggguagggcccgugacug
gggcgaagucguagcuguaccggaaggugcggcugga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7v2o Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): G2 P7 V8 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 G41 Q42 H43 Y54 A55 L58 R59 Q62 R65 S71 E72 R73 Q74 V112 R115 Q116 Q119 R122 H123 H125 R132 D134 L135 S137 Y138 R141 K151 L157 E205 R209
• Binding residue (residue number reindexed from 1): G1 P6 V7 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 G40 Q41 H42 Y53 A54 L57 R58 Q61 R64 S70 E71 R72 Q73 V111 R114 Q115 Q118 R121 H122 H124 R131 D133 L134 S136 Y137 R140 K150 L156 E204 R208

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

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

External links

• PDB: RCSB:7v2o, PDBe:7v2o, PDBj:7v2o
• PDBsum: 7v2o
• PubMed: 35316014
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)