Structure of PDB 6b4v Chain MA Binding Site BS01

Receptor Information

>6b4v Chain MA (length=208) Species: 262724 (Thermus thermophilus HB27)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

Ligand information

>6b4v Chain A (length=1507)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcgggguuuuacuccguggucagcggcggac
gggugaguaacgcgugggugaccuacccggaagagggggacaacccgggg
aaacucgggcuaaucccccauguggacccgccccuugggguguguccaaa
gggcuuugcccgcuuccggaugggcccgcgucccaucagcuaguuggugg
gguaauggcccaccaaggcgacgacggguagccggucugagaggauggcc
ggccacaggggcacugagacacgggccccacuccuacgggaggcagcagu
uaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuugga
ggaagaagcccuucgggguguaaacuccugaacccgggacgaaacccccg
aggaggggacugacgguaccgggguaauagcgccggccaacuccgugcca
gcagccgcgguaauacggagggcgcgagcguuacccggauucacugggcg
uaaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuc
aaccgugggggagcgugggauacgcucaggcuagacggugggagagggug
guggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgcc
gauggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagc
guggggagcaaaccggauuagauacccggguaguccacgcccuaaacgau
gcgcgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcg
cgccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacgg
gggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaag
aaccuuaccaggccuugacaugcuagggaacccgggugaaagccuggggu
gccccgcgaggggagcccuagcacaggugcugcauggccgucgucagcuc
gugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccgu
uaguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagc
gggaggaaggaggggacgacgucuggucagcauggcccuuacggccuggg
cgacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacgg
ggagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaaccc
gaccccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcgg
ugaauacguucccgggccuuguacacaccgcccgucacgccaugggagcg
ggcucuacccgaagucgccgggagccuacgggcaggcgccgaggguaggg
cccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcgg
cuggauc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6b4v Mechanism of Inhibition of Translation Termination by Blasticidin S.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 G23 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 K46 Y54 A55 R59 Q62 E72 R73 Q74 K84 S113 R115 Q116 R118 Q119 R122 H123 H125 R131 R132 V133 D134 L135 P136 S137 Y138 L157 E205 R209
• Binding residue (residue number reindexed from 1): G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 G22 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 K45 Y53 A54 R58 Q61 E71 R72 Q73 K83 S112 R114 Q115 R117 Q118 R121 H122 H124 R130 R131 V132 D133 L134 P135 S136 Y137 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:6b4v, PDBe:6b4v, PDBj:6b4v
• PDBsum: 6b4v
• PubMed: 29366636
• UniProt: P62664|RS4_THET2 Small ribosomal subunit protein uS4 (Gene Name=rpsD)