Structure of PDB 7ryf Chain K Binding Site BS01

Receptor Information

>7ryf Chain K (length=144) Species: 480119 (Acinetobacter baumannii AB0057)

TLRLNELAPAEGAKREHRRLGRGIGSGVGKTGGRGIKGQKSRKSGGVRPG
FEGGQTAIYRRLPKFGFTSQIALKTAEVRLSELSKVEGDIVSLETLKAAN
VVRRDQIRARIVLSGEITRAFTVQGVALTKGAKAAIEAAGGKVE

Ligand information

>7ryf 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: 7ryf An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): L5 N6 E12 G13 A14 K15 R16 R19 R20 L21 G22 R23 G24 G26 S27 G30 K31 T32 G34 R35 K38 G39 Q40 K41 R43 K44 S45 R49 E53 G54 Q56 T57 Y60 R61 R62 P64 K65 F66 G67 F68 S70 E78 R80 E83 K86 N101 R104 R105 R109 R111 V113 L114 S115 T130 G132
• Binding residue (residue number reindexed from 1): L4 N5 E11 G12 A13 K14 R15 R18 R19 L20 G21 R22 G23 G25 S26 G29 K30 T31 G33 R34 K37 G38 Q39 K40 R42 K43 S44 R48 E52 G53 Q55 T56 Y59 R60 R61 P63 K64 F65 G66 F67 S69 E77 R79 E82 K85 N100 R103 R104 R108 R110 V112 L113 S114 T129 G131

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:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7ryf, PDBe:7ryf, PDBj:7ryf
• PDBsum: 7ryf
• PubMed: 35100868
• UniProt: B7IA20|RL15_ACIB5 Large ribosomal subunit protein uL15 (Gene Name=rplO)