Structure of PDB 4z8c Chain 1d Binding Site BS01

Receptor Information

>4z8c Chain 1d (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

Ligand information

>4z8c Chain 1a (length=1477)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccucgggaggcagcaguuaggaauc
uuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaag
cccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggg
acugacgguaccgggguaauagcgccggccaacuccgugccagcagccgc
gguaauacggagggcgcgagcguuacccggauucacugggcguaaagggc
guguaggcggccuggggcgucccaugugaaagaccacggcucaaccgugg
gggagcgugggauacgcucaggcuagacggugggagagggugguggaauu
cccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcga
aggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggag
caaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcua
ggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccu
ggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgc
acaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuac
caggccuugacaugcuagggaacccgggugaaagccugggccuagcacag
gugcugcauggccgucgucagcucgugccgugagguguuggguuaagucc
cgcaacgagcgcaacccccgccguuaguugccagcgguucggccgggcac
ucuaacgggacugcccgcgaaagcgggaggaaggaggggacgacgucugg
ucagcauggcccuuacggccugggcgacacacgugcuacaaugcccacua
caaagcgaugccacccggcaacggggagcuaaucgcaaaaaggugggccc
aguucggauuggggucugcaacccgaccccaugaagccggaaucgcuagu
aaucgcggaucagccaugccgcggugaauacguucccgggccuuguacac
accgcccgucacgccaugggagcgggcucuacccgaagucgccgggagcc
uacgggcaggcgccgaggguagggcccgugacuggggcggucguaacaag
guagcuguaccggaaggugcggcugga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4z8c The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 E24 R25 R35 R36 Y38 P40 G41 Q42 H43 S52 Y54 A55 R59 Q62 E72 R73 Q74 V112 S113 R115 Q116 R118 Q119 R122 H123 H125 R132 D134 S137 R141 L155 S208 R209
• Binding residue (residue number reindexed from 1): G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 E23 R24 R34 R35 Y37 P39 G40 Q41 H42 S51 Y53 A54 R58 Q61 E71 R72 Q73 V111 S112 R114 Q115 R117 Q118 R121 H122 H124 R131 D133 S136 R140 L154 S207 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:4z8c, PDBe:4z8c, PDBj:4z8c
• PDBsum: 4z8c
• PubMed: 25984972
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)