Structure of PDB 4z8c Chain 2R Binding Site BS01

Receptor Information

>4z8c Chain 2R (length=118) Species: 300852 (Thermus thermophilus HB8)

MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDH
LIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKL
AERRRGDGAPLALVELVE

Ligand information

>4z8c Chain 2A (length=2790)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccauc
cuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcuuaagcccagcgccgaagcugcgggucuggggccccaggc
gguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcu
ggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggguga
gaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcg
uaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggca
gccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucua
ggcuagggggaccggagccauggacgagcccggccagaagcgcagggugg
gagguaggcaaauccgccucccaacaagcucugcgugguggggaagcccg
cgggugacaaccccccgaagccagggagccaagaaaagccucuaagcaca
accugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagag
cacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccc
cguaacuucgggagaaggggugcucccuggggugaugagccccggggagc
cgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcg
aacucguaagaggagguauagggagcgacgcuugcccggugccggaaggu
caaggggaggggugcaagccccgaaccgaagccccggugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgg
ugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaa
gaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcggc
ugggggccuaacccucggauggggggacagcgcuuggcgggcaguuugac
uggggcggucgccuccuaaaagguaacggaggcgcccaaagguccccuca
ggcgggacggaaauccgccggagagcgcaaggguagaagggggccugacu
gcgaggccugcaagccgagcaggggcgaaagccgggccuagugaaccggu
ggucccguguggaagggccaucgaucaacggauaaaaguuaccccgggga
uaacaggcugaucucccccgagcguccacagcggcggggagguuuggcac
cucgaugucggcucgucgcauccuggggcugaagaaggucccaaggguug
ggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucguga
gacaguucggucucuauccgccacgggcgcaggaggcuugaggggggcuc
uuccuaguacgagaggaccggaagggacgcaccucugguuucccagcugu
cccuccaggggcauaagcuggguagccaugugcggaagggauaaccgcug
aaagcaucuaagcgggaagcccgccccaagaugaggccucccggcagccg
guaaggacccgggaagaccacccgguggaugggccggggguguaagcgcc
gcgaggcguugagccgaccggucccaaucguccgaggucu

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

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): M1 R2 H3 L4 K5 S6 R8 K9 L10 N11 R12 H13 S14 S15 H16 R17 A19 R22 N23 Q24 K26 S27 H31 I34 T35 T36 T37 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 R77 R90 Q91 G92 G93 R96 K99 R104 R105 G106 D107
• Binding residue (residue number reindexed from 1): M1 R2 H3 L4 K5 S6 R8 K9 L10 N11 R12 H13 S14 S15 H16 R17 A19 R22 N23 Q24 K26 S27 H31 I34 T35 T36 T37 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 R77 R90 Q91 G92 G93 R96 K99 R104 R105 G106 D107

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4z8c, PDBe:4z8c, PDBj:4z8c
• PDBsum: 4z8c
• PubMed: 25984972
• UniProt: Q9Z9H5|RL17_THET8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)