Structure of PDB 6v3d Chain I Binding Site BS01

Receptor Information

>6v3d Chain I (length=142) Species: 480119 (Acinetobacter baumannii AB0057)

MKTLSAKPAEVQHDWFVVDATGKTLGRLATEIARRLRGKHKTSYTPHVDT
GDYIIVINAEQVQVTGNKALDKKYYRHTEFPGGLKETNFEKLVAHKPEEI
FERAVKGMLPKGPLGYAMIKKMKVYAGSEHPHAAQQPQVLDI

Ligand information

>6v3d 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: 6v3d Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): M1 T3 K7 W15 T24 G26 R27 T30 R37 K39 H47 Y53 T65 K68 K72 Y75 R76 H77 T78 F80 A104 G107 M108 K111 P113 L114 Y116 H132 A134 Q135
• Binding residue (residue number reindexed from 1): M1 T3 K7 W15 T24 G26 R27 T30 R37 K39 H47 Y53 T65 K68 K72 Y75 R76 H77 T78 F80 A104 G107 M108 K111 P113 L114 Y116 H132 A134 Q135

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6v3d, PDBe:6v3d, PDBj:6v3d
• PDBsum: 6v3d
• PubMed: 31964740
• UniProt: B7I9B0|RL13_ACIB5 Large ribosomal subunit protein uL13 (Gene Name=rplM)