Structure of PDB 8p17 Chain B Binding Site BS01

Receptor Information

>8p17 Chain B (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>8p17 Chain 2 (length=1536)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaauucuuugcugacgaguggc
ggacgggugaguaaugucugggaaacugccugauggagggggauaacuac
uggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagggggac
cuucgggccucuugccaucggaugugcccagaugggauuagcuaguaggu
gggguaacggcucaccuaggcgacgaucccuagcuggucugagaggauga
ccagccacacuggaacugagacacgguccagacuccuacgggaggcagca
guggggaauauugcacaaugggcgcaagccugaugcagccaugccgcgug
uaugaagaaggccuucggguuguaaaguacuuucagcggggaggaaggga
guaaaguuaauaccuuugcucauugacguuacccgcagaagaagcaccgg
cuaacuccgugccagcagccgcgguaauacggagggugcaagcguuaauc
ggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucagaugug
aaauccccgggcucaaccugggaacugcaucugauacuggcaagcuugag
ucucguagagggggguagaauuccagguguagcggugaaaugcguagaga
ucuggaggaauaccgguggcgaaggcggcccccuggacgaagacugacgc
ucaggugcgaaagcguggggagcaaacaggauuagauacccugguagucc
acgccguaaacgaugucgacuuggagguugugcccuugaggcguggcuuc
cggagcuaacgcguuaagucgaccgccuggggaguacggccgcaagguua
aaacucaaaugaauugacgggggcccgcacaagcgguggagcaugugguu
uaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacggaag
uuuucagagaugagaaugugccuucgggaaccgugagacaggugcugcau
ggcugucgucagcucguguugugaaauguuggguuaagucccgcaacgag
cgcaacccuuauccuuuguugccagcgguccggccgggaacucaaaggag
acugccagugauaaacuggaggaagguggggaugacgucaagucaucaug
gcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaagaga
agcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccgga
uuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgugg
aucagaaugccacggugaauacguucccgggccuuguacacaccgcccgu
cacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucggga
gggcgcuuaccacuuugugauucaugacuggggugaagucguaacaaggu
aaccguaggggaaccugcgguuggaucaccuccuua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p17 The compensatory mechanism of a naturally evolved E167K RF2 counteracting the loss of RF1 in bacteria
• Resolution: 2.78 Å
• Binding residue (original residue number in PDB): R175 M201
• Binding residue (residue number reindexed from 1): R174 M200

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p17, PDBe:8p17, PDBj:8p17
• PDBsum: 8p17
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)