Structure of PDB 6qul Chain D Binding Site BS01

Receptor Information

>6qul Chain D (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

Ligand information

>6qul Chain A (length=2795)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuggcgu
gugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagca
agguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcgu
uaaguugcaggguauagacccgaaacccggugaucuagccaugggcaggu
ugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaa
auuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggaga
uagcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucu
ccggggguagagcacuguuucggcaagggggcuuaccaacccgaugcaaa
cugcgaauaccggagaauguuaucacgggagacacacggcgggugcuaac
guccgucgugaagagggaaacaacccagaccgccagcuaaggucccaaag
ucaugguuaagugggaaacgaugugggaaggcccagacagccaggauguu
ggcuuagaagcagccaucauuuaaagaaagcguaauagcucacuggucga
gucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugc
ggcagcgacgcugcguuguuggguaggggagcguucuguaagccugcgaa
ggugugcugugaggcaugcuggagguaucagaagugcgaaugcugacaua
aguaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuc
cuguccaacguuaaucggggcagggugagucgaccccuaaggcgaggccg
aaaggcguagucgaugggaaacagguuaauauuccuguacuugguguuac
ugcgaaggggggacggagaaggcuauguuggccgggcgacgguugucccg
guuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcug
aggcgugaugacgaggcgcugaagcaacaaaugcccugcuuccaggaaaa
gccucuaagcaucagguaacaucaaaucguaccccaaaccgacacaggug
gucagguagagaauaccaaggcgcuugagagaacucgggugaaggaacua
ggcaaaauggugccguaacuucgggagaaggcacgcugauauguagguga
ggucccucgcggauggagcugaaaucagucgaagauaccagcuggcugca
acuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguauac
ggugugacgccugcccggugccggaagguuaauugaugggguuagcgcaa
gcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaacgg
uccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaug
gcguaaugauggccaggcugucuccacccgagacucagugaaauugaacu
cgcugugaagaugcaguguacccgcggcaagacggaaagaccccgugaac
cuuuacuauagcuugacacugaacauugauugauguucuaacguugaccc
guaauccggguugcggacagugucugguggguaguuugacuggggcgguc
uccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucgg
acaucaggagguuagugcaauggcauaagccagcuugacugcgagcguga
cggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaau
ggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcug
auaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucg
gcucaucacauccuggggcugaaguaggucccaaggguauggcuguucgc
cauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgg
ucccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguac
gagaggaccggaguggacgcaucacugguguucggguugucaugccaaug
gcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaa
gcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccug
aaggaacguugaagacgacgacguugauaggccggguguguaagcgcagc
gaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qul Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): M11 T12 R13 P23 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 K114 G115 K116 G117 F118 G120 R124 N126 F127 R128 T129 Q130 D131 T133 H134 G135 N136 S137 L138 S139 H140 R141 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 K190 A192 V193 P194 T197 K208
• Binding residue (residue number reindexed from 1): M11 T12 R13 P23 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 K114 G115 K116 G117 F118 G120 R124 N126 F127 R128 T129 Q130 D131 T133 H134 G135 N136 S137 L138 S139 H140 R141 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 K190 A192 V193 P194 T197 K208

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6qul, PDBe:6qul, PDBj:6qul
• PDBsum: 6qul
• PubMed: 30948752
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)