Structure of PDB 7m4w Chain D Binding Site BS01

Receptor Information

>7m4w Chain D (length=211) Species: 480119 (Acinetobacter baumannii AB0057)

AIGLVGRKCGMTRIFTDAGVSVPVTVIEVDPNRITQIKTLETDGYQAVQV
TTGERRESRVTNAQKGHFAKAGVAAGRLVKEFRVTEAELEGREVGGTIGV
DLFTVGQIVDVTGQSKGKGFQGGVKRWNFRTQDATHGNSVSHRVLGSTGQ
NQTPGRVFKGKKMAGHLGDERVTVQGLEIVSVDTERSVLVVKGAIPGATG
GDVIVRPTIKA

Ligand information

>7m4w Chain A (length=2730)

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
uaaaucagccuggcguugguuguccaggugaaaggauguaggcauguauc
uuaggcaaauccgggguacucuaugcugagaucugauagcaagcuguacu
ugugcagcgaagugguugaugccaugcuuccaggaaaagucucuaagcuu
caguuacacaggaaucguacccgaaaccgacacagguggucaggucgagu
agaccaaggcgcuugagagaacucugcugaaggaacuaggcaaaauggua
ccguaacuucgggagaagguacgcuguuguuggugauggaacucgcuucc
ugagcugacgacagccgcagaaaccaggccgcugcaacuguuuauuaaaa
acauagcacucugcaaacacgaaaguggacguauagggugugaugccugc
ccggugcuggaagguuaauugaugggguuagcguaagcgaagcucuugau
cgaagccccaguaaacggcggccguaacuauaacgguccuaagguagcga
aauuccuugucggguaaguuccgaccugcacgaauggcauaaugauggcg
gcgcugucuccagcagaggcucagugaaaucgaaaucgcugugaagaugc
aguguacccgcggcuagacggaaagaccccgugaaccuuuacugcagcuu
gacacugaacuuugauugagguucuaacucugucccgugauccgggacga
ggaccgugucugguggguaguuugacuggggcggucuccuccuaaagagu
aacggaggaguacgaaggugcgcucagcguggucggaaaucacgcguaga
guauaaaggcaaaagcgcgcuuaacugcgagacccacaagucgagcaggu
acgaaaguaggucuuagugauccggugguucuguauggaagggccaucgc
ucaacggauaaaagguacucuggggauaacaggcugauaccgcccaagag
uucauaucgacggcgguguuuggcaccucgaugucggcucaucucauccu
ggggcugaagcaggucccaaggguauggcuguucgccauuuaaagaggua
cgcgagcuggguuuagaacgucgugagacaguucggucccuaucuaccgu
gggcgcuggaaauuugagaggaucugcuccuaguacgagaggaccagagu
ggacgaaccucugguguaccgguugugacgccagucgcaucgccggguag
cuauguucggaagggauaaccgcugaaagcaucuaagcgggaagccuacc
ucaagauaagauuucccuaggacuuuauguccucuaaagagccguucgag
acuaggacguugauagguuggauguggaagcauagugauaugugaagcug
accaauacuaauugcucgugaggcuugacu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m4w Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): M12 R14 Q37 D44 Y46 R56 R57 R60 N63 A64 Q65 H68 K71 E82 R84 K117 G118 K119 G120 F121 Q122 G123 R127 R131 T132 A135 T136 H137 G138 S140 V141 S142 H143 R144 S148 T149 G150 Q151 N152 Q153 T154 P155 G156 R157 V158 K160 G161 K162 M164 A165 H167 R172 Q176 I196 T200 K211
• Binding residue (residue number reindexed from 1): M11 R13 Q36 D43 Y45 R55 R56 R59 N62 A63 Q64 H67 K70 E81 R83 K116 G117 K118 G119 F120 Q121 G122 R126 R130 T131 A134 T135 H136 G137 S139 V140 S141 H142 R143 S147 T148 G149 Q150 N151 Q152 T153 P154 G155 R156 V157 K159 G160 K161 M163 A164 H166 R171 Q175 I195 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:7m4w, PDBe:7m4w, PDBj:7m4w
• PDBsum: 7m4w
• PubMed: 34044590
• UniProt: B7IA39|RL3_ACIB5 Large ribosomal subunit protein uL3 (Gene Name=rplC)