Structure of PDB 6pc5 Chain L Binding Site BS01

Receptor Information

>6pc5 Chain L (length=144) Species: 562 (Escherichia coli)

MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGF
EGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANI
IGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE

Ligand information

>6pc5 Chain I (length=2897)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auguguaggauaggugggaggcuuugaaguguggacgccagucugcaugg
agccgaccuugaaauaccacccuuuaauguuugauguucuaacguugacc
cguaauccggguugcggacagugucugguggguaguuugacuggggcggu
cuccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucg
gacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgug
acggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaa
uggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcu
gauaccgcccaagaguucauaucgacggcgguguuuggcaccucgauguc
ggcucaucacauccuggggcugaaguaggucccaaggguauggcuguucg
ccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucg
gucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagua
cgagaggaccggaguggacgcaucacugguguucggguugucaugccaau
ggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucua
agcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccu
gaaggaacguugaagacgacgacguugauaggccggguguguaagcgcag
cgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pc5 Synthetic group A streptogramin antibiotics that overcome Vat resistance.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): L3 N4 E10 G11 S12 K13 K14 K17 R18 L19 G20 R21 G22 G24 S25 K29 T30 G32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 R47 R48 F50 G53 Q54 M55 Y58 R59 R60 L61 P62 K63 F64 G65 F66 T67 S68 R69 E76 R78 N99 Q104 K109 I111 L112 R126 T128 K129
• Binding residue (residue number reindexed from 1): L3 N4 E10 G11 S12 K13 K14 K17 R18 L19 G20 R21 G22 G24 S25 K29 T30 G32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 R47 R48 F50 G53 Q54 M55 Y58 R59 R60 L61 P62 K63 F64 G65 F66 T67 S68 R69 E76 R78 N99 Q104 K109 I111 L112 R126 T128 K129

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6pc5, PDBe:6pc5, PDBj:6pc5
• PDBsum: 6pc5
• PubMed: 32968273
• UniProt: P02413|RL15_ECOLI Large ribosomal subunit protein uL15 (Gene Name=rplO)