Structure of PDB 7ryg Chain D Binding Site BS01

Receptor Information

>7ryg Chain D (length=211) Species: 480119 (Acinetobacter baumannii AB0057)

AIGLVGRKCGMTRIFTDAGVSVPVTVIEVDPNRITQIKTLETDGYQAVQV
TTGERRESRVTNAQKGHFAKAGVAAGRLVKEFRVTEAELEGREVGGTIGV
DLFTVGQIVDVTGQSKGKGFQGGVKRWNFRTQDATHGNSVSHRVLGSTGQ
NQTPGRVFKGKKMAGHLGDERVTVQGLEIVSVDTERSVLVVKGAIPGATG
GDVIVRPTIKA

Ligand information

>7ryg Chain A (length=2685)

gucaaguaauuaagugcaugugguggaugccuuggcagucagaggcgaug
aaagacgugauagccugcgaaaagcuccggggaggcggcaaauauccuuu
gauccggagaugucugaaugggggaacccaccuacuuuaagguagguauu
gcaacaugaauacauaguguugcaaggcgaacgaggggaagugaaacauc
ucaguacccuuaggaaaagaaaucaauugagauucccucaguagcggcga
gcgaacggggaucagcccauuaaguuauguguguuuuaguggaacgcucu
gggaagugcgaacguagagggugauauucccguacacgaaagggcacaca
uaaugaugacgaguagggcgaggcacgugaaaccuugucugaauaugggg
ggaccauccuccaaggcuaaauacuccugacugaccgauagugaaccagu
accgugagggaaaggcgaaaagaaccccugugaggggagugaaauagauc
cugaaaccgcaugcauacaagcagugggagcaccuucguggugugacugc
guaccuuuuguauaaugggucagcgacuuauauucaguagcgagguuaac
cguauaggggagccguagagaaaucgagucuuaauagggcguuuaguugc
uggguauagacccgaaaccaggcgaucuauccaugagcagguugaagguu
ggguaacacuaacuggaggaccgaacccacugucguugaaaagccagggg
augacuuguggauaggggugaaaggcuaaucaagccuggugauagcuggu
ucuccccgaaagcuauuuagguagcgccucggacgaauaccauagggggu
agagcacuguuucggcaccgaugcaaacuccgaauaccuaugaguacuau
ccgggagacagacugcgggugcuaacguccguagucaagaggaaaacaau
ccagaccgccagcuaaggccccaaaaucauaguuaagugggaaacgaugu
gggaaggcauagacagcuauagucgagucggccugcgcggaagauguaac
ggggcuaaaacuaugugccgaagcugcggauguauacuuuguauacgugg
uaggggagcguucuguaagccgaugaagguguguugagaagcaugcugga
gguaucagaagugcgaaugcugacgugaguaacgacaaaacgggugaaaa
acccguucgccgaaagaccaaggguuccaguccaacguuaaucggggcug
ggugagucgaccccuaaggcgaggccgaaaggcguagucgaugggaaaau
gguuaauauuccauuacuucuguguaaugcgaugagaggacggagaaggc
uaaaucagccuggcguugguuguccaggugaaaggauguaggcaaugcug
agaucugauagcaagcuguacuugugcagcgaagugguugaugccaugcu
uccaggaaaagucucuaagcuucaguuacacaggaaucguacccgaaacc
gacacagguggucaggucgaguagaccaaggcgcuugagagaacucugcu
gaaggaacuaggcaaaaugguaccguaacuucgggagaagguacgcuguu
guuggugauggaacucgcuuccugagcugacgacagccgcagaaaccagg
ccgcugcaacuguuuauuaaaaacauagcacucugcaaacacgaaagugg
acguauagggugugaugccugcccggugcuggaagguuaauugauggggu
uagcguaagcgaagcucuugaucgaagccccaguaaacggcgccuaaggu
agcgaaauuccuugucggguaaguuccgaccugcacgaauggcauaauga
uggcggcgcugucuccagcagaggcucagugaaaucgaaaucgcugugaa
gaugcaguguacccgcggcuagacggaaagaccccgugaaccuuuacugc
agcuugacacugaacuuugauugagguucuaacucugucccgugauccgg
gacgaggaccgugucugguggguaguuugacuggggcggucuccuccuaa
agaguaacggaggaguacgaaggugcgcucagcguggucggaaaucacgc
guagaguauaaaggcaaaagcgcgcuuaacugcgagacccacaagucgag
cagguacgaaaguaggucuuagugauccggugguucuguauggaagggcc
aucgcucaacggauaaaagguacucuggggauaacaggcugauaccgccc
aagaguucauaucgacggcgguguuuggcaccucgaugucggcucaucuc
auccuggggcugaagcaggucccaaggguauggcuguucgccauuuaaag
agguacgcgagcuggguuuagaacgucgugagacaguucggucccuaucu
accgugggcgcuggaaauuugagaggaucugcuccuaguacgagaggacc
agaguggacgaaccucugguguaccgguugugacgccagucgcaucgccg
gguagcuauguucggaagggauaaccgcugaaagcaucuaagcgggaagc
cuaccucaagauaagauuucccuaggacuuuauguccucuaaagagccgu
ucgagacuaggacguugauagguuggauguggaagcauagugauauguga
agcugaccaauacuaauugcucgugaggcuugacu

<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<....
..<<<<<<....(((.>>>.....<<<<<<<..<<.)))......>>...
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>
......>>>>>.>.........<<....>>...<<<<<.....<<.....
>>....>>>>>...<<<......<<<<<<<<<<<<<<.<<<...<<<.<.
.....>.>>>((......<<<.....))>>>...>>>...>>>>>>>>>>
>>>>...........<<<<<<<<.........>>>>>>>>......<<<<
<..<<<<>>>>>..>>>......]].>>>>>>>.]]..............
.<<....>>....]].........<<<<.....>>>>.............
}....>>>>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>
...<.<........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<
<.....>>...>>>...<<....>>..<<<<.....>>>>.....>>>>>
>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<
<<......>>>>>>.....>>>...<<<.<<<.<........>.>>>>>>
....>>>>>>>>>...<<<.....>>>......>>>>>>...>..>.>>.
.<<<<<<....<<<<<....>>>>>.<<<<<<<....<<<<<<<<<....
.<<<...<<<.<<<<..>>>>.>>>..>>.>.....>>>>>>.>>>...>
>>>>>.>...<<<<<<<<<<......>>>>>>>>>>....<<<......>
>>...<<<<.<<<...<<<(((.....<<<<<<...........<<.<<<
<<<..<<.........<<..>>.....>>..>>>>>>>>...........
)))......>>>>>>.>>>...>>>>>>><<<<<<<.....>>>>>>>..
..>>>>>><.<<<<<...<<<......<<<<<<<<....>>>>>>>>...
>>>..>>>>>..>.....>>>>>><......<<.....<<<<<<......
.>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>
>....((<<<.<<<...<<<...<<<....>>>...>>>...>>>..<<<
<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<
..<<<<<<<<<<<...((((...>>>>>>....<<<<...<<<<.>>>>.
..>>>>........<<<<<......>>>>>....>>>>>...>>>...>>
>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<
<.<<...............<<<<<.....<..>......>>>>><<<<<<
<<<<<<...<<<<.....>>>>...>>>>>>>>>>>>............<
<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>.
......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<........<<<<<
..<<....>>...>>>>>........>>>>>>>>..>>>>>.........
.<...........<<<<<<.....>>>>>>.....>....>>>>>..>>.
>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<....
....>>>>>..<<<<<<<.<<<<.[[......<<<<.[[<<<<..<<<<.
.<<<.<<<<<.<<<<<<<<..>>>>>>>>...<<<.<<<<<<.....>>>
>>>>>>....>>>>>.>>>...>>>>..<<<<.....>>>><<<<<<...
........>>>>>>..<<...<<<<<<<..<<<<<<<.......>>>>>>
.>...<<.[.(((>>....>>>>>>>...<<<<..<<<......>>>..>
>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>>>..))>>>
>>>>.............>>>>..]]>>>>.......<<<<.<.<<<<<<.
..<<.......>>...>>>>>>...>>>>.>.......<<<<<.<<<<<<
..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>
>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]..>>>
>>>>>>>>....<<<<<<<...<<<<..<<<<<<................
.>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))))>>>>>>..>>>>
>...>>>>.>>>>>...<<<....<<<<<...........>>>>>....>
>>.>>>>.......>>>>>>>..<<<<<.....>>>>><....<<<<<<<
<<.......>>>>>....<<<<<<<<..<<....<<<<<....>>>>>..
.>>...>>>>>.>>>...>>>>..>..>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ryg An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii.
• Resolution: 2.38 Å
• Binding residue (original residue number in PDB): M12 T13 Q37 D44 Y46 R56 R57 R60 N63 A64 Q65 G67 H68 K71 E82 R84 K117 G118 K119 G120 F121 Q122 R127 R131 T132 Q133 A135 T136 H137 G138 S140 V141 S142 H143 R144 G147 S148 T149 G150 Q151 N152 Q153 T154 P155 G156 R157 V158 K160 K162 M164 A165 H167 R172 T174 Q176 T200 K211
• Binding residue (residue number reindexed from 1): M11 T12 Q36 D43 Y45 R55 R56 R59 N62 A63 Q64 G66 H67 K70 E81 R83 K116 G117 K118 G119 F120 Q121 R126 R130 T131 Q132 A134 T135 H136 G137 S139 V140 S141 H142 R143 G146 S147 T148 G149 Q150 N151 Q152 T153 P154 G155 R156 V157 K159 K161 M163 A164 H166 R171 T173 Q175 T199 K210

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:7ryg, PDBe:7ryg, PDBj:7ryg
• PDBsum: 7ryg
• PubMed: 35100868
• UniProt: B7IA39|RL3_ACIB5 Large ribosomal subunit protein uL3 (Gene Name=rplC)