Structure of PDB 6v39 Chain G Binding Site BS01

Receptor Information

>6v39 Chain G (length=174) Species: 480119 (Acinetobacter baumannii AB0057)

SRVAKAPVTVPNGVTVTQNGRQVEVKGSKGTLSFNLHALVELKQEEGKLQ
LAPAKESKDAWMQAGTARAVLNNLVKGVSEGFERKLQLVGVGYKAAVKGT
VVNLNLGYSHPIDYALPEGVTAETPTATEIILKSANKQLLGQVAAEIRAY
RSPEPYKGKGVRYSDEVILRKEAK

Ligand information

>6v39 Chain AN1 (length=2892)

agucaaguaauuaagugcaugugguggaugccuuggcagucagaggcgau
gaaagacgugauagccugcgaaaagcuccggggaggcggcaaauauccuu
ugauccggagaugucugaaugggggaacccaccuacuuuaagguagguau
ugcaacaugaauacauaguguugcaaggcgaacgaggggaagugaaacau
cucaguacccuuaggaaaagaaaucaauugagauucccucaguagcggcg
agcgaacggggaucagcccauuaaguuauguguguuuuaguggaacgcuc
ugggaagugcgaacguagagggugauauucccguacacgaaagggcacac
auaaugaugacgaguagggcgaggcacgugaaaccuugucugaauauggg
gggaccauccuccaaggcuaaauacuccugacugaccgauagugaaccag
uaccgugagggaaaggcgaaaagaaccccugugaggggagugaaauagau
ccugaaaccgcaugcauacaagcagugggagcaccuucguggugugacug
cguaccuuuuguauaaugggucagcgacuuauauucaguagcgagguuaa
ccguauaggggagccguagagaaaucgagucuuaauagggcguuuaguug
cuggguauagacccgaaaccaggcgaucuauccaugagcagguugaaggu
uggguaacacuaacuggaggaccgaacccacugucguugaaaagccaggg
gaugacuuguggauaggggugaaaggcuaaucaagccuggugauagcugg
uucuccccgaaagcuauuuagguagcgccucggacgaauaccauaggggg
uagagcacuguuucggcuagggggucaucccgacuuaccaaaccgaugca
aacuccgaauaccuaugaguacuauccgggagacagacugcgggugcuaa
cguccguagucaagaggaaaacaauccagaccgccagcuaaggccccaaa
aucauaguuaagugggaaacgaugugggaaggcauagacagcuaggaggu
uggcuuagaagcagccacccuuuaaagaaagcguaauagcucacuagucg
agucggccugcgcggaagauguaacggggcuaaaacuaugugccgaagcu
gcggauguauacuuuguauacgugguaggggagcguucuguaagccgaug
aagguguguugagaagcaugcuggagguaucagaagugcgaaugcugacg
ugaguaacgacaaaacgggugaaaaacccguucgccgaaagaccaagggu
uccaguccaacguuaaucggggcugggugagucgaccccuaaggcgaggc
cgaaaggcguagucgaugggaaaaugguuaauauuccauuacuucugugu
aaugcgaugagaggacggagaaggcuaaaucagccuggcguugguugucc
aggugaaaggauguaggcauguaucuuaggcaaauccgggguacucuaug
cugagaucugauagcaagcuguacuuguacagcgaagugguugaugccau
gcuuccaggaaaagucucuaagcuucaguuacacaggaaucguacccgaa
accgacacagguggucaggucgaguagaccaaggcgcuugagagaacucu
gcugaaggaacuaggcaaaaugguaccguaacuucgggagaagguacgcu
guuguuggugauggaacucgcuuccugagcugacgacagccgcagaaacc
aggccgcugcaacuguuuauuaaaaacauagcacucugcaaacacgaaag
uggacguauagggugugaugccugcccggugcuggaagguuaauugaugg
gguuagcguaagcgaagcucuugaucgaagccccaguaaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaauggcauaaugauggcggcgcugucuccagcagaggcucagu
gaaaucgaaaucgcugugaagaugcaguguacccgcggcuagacggaaag
accccgugaaccuuuacugcagcuugacacugaacuuugaccuuacuugu
guaggauaggugggaggcuuugaagcuggaacgcuaguuccaguggagcc
guccuugaaauaccacccugguaauguugagguucuaacucugucccgug
auccgggacgaggaccgugucugguggguaguuugacuggggcggucucc
uccuaaagaguaacggaggaguacgaaggugcgcucagcguggucggaaa
ucacgcguagaguauaaaggcaaaagcgcgcuuaacugcgagacccacaa
gucgagcagguacgaaaguaggucuuagugauccggugguucuguaugga
agggccaucgcucaacggauaaaagguacucuggggauaacaggcugaua
ccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucggcu
caucucauccuggggcugaagcaggucccaaggguauggcuguucgccau
uuaaagagguacgcgagcuggguuuagaacgucgugagacaguucggucc
cuaucuaccgugggcgcuggaaauuugagaggaucugcuccuaguacgag
aggaccagaguggacgaaccucugguguaccgguugugacgccagucgca
ucgccggguagcuauguucggaagggauaaccgcugaaagcaucuaagcg
ggaagccuaccucaagauaagauuucccuaggacuuuauguccucuaaag
agccguucgagacuaggacguugauagguuggauguggaagcauagugau
augugaagcugaccaauacuaauugcucgugaggcuugacua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6v39 Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): S2 R3 V4 K59 M63 T67 A70 N74 Y109 S110 H111 Q139 G142 Y157 K172 A174
• Binding residue (residue number reindexed from 1): S1 R2 V3 K58 M62 T66 A69 N73 Y108 S109 H110 Q138 G141 Y156 K171 A173

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6v39, PDBe:6v39, PDBj:6v39
• PDBsum: 6v39
• PubMed: 31964740
• UniProt: B7IA24|RL6_ACIB5 Large ribosomal subunit protein uL6 (Gene Name=rplF)