Structure of PDB 6pc8 Chain K Binding Site BS01

Receptor Information

>6pc8 Chain K (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>6pc8 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: 6pc8 Synthetic group A streptogramin antibiotics that overcome Vat resistance.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): P8 T9 P11 G12 R13 R14 H15 E35 S40 R43 N44 N45 N46 R48 I49 T50 T51 R52 H53 G56 H58 K59 Q60 Y62 R63 Y83 P85 R87 D98 G99 R101 M146 K147 G149 K150 Q153 L154 A155 R156 S157 G159 T160 Y171 L176 R177 S178 E180 R182 H200 M201 G206 K207 A208 G209 R212 W213 R214 R217 P218 T219 V220 R221 T223 A224 M225 N226 P227 V228 D229 H232 G234 G235 E236 R238 N239 F240 G241 K242 H243 P244 T246 W248 Q251 T252 K253 G254 K256 T257 R258 S259 K261 R262 R270 R271
• Binding residue (residue number reindexed from 1): P7 T8 P10 G11 R12 R13 H14 E34 S39 R42 N43 N44 N45 R47 I48 T49 T50 R51 H52 G55 H57 K58 Q59 Y61 R62 Y82 P84 R86 D97 G98 R100 M145 K146 G148 K149 Q152 L153 A154 R155 S156 G158 T159 Y170 L175 R176 S177 E179 R181 H199 M200 G205 K206 A207 G208 R211 W212 R213 R216 P217 T218 V219 R220 T222 A223 M224 N225 P226 V227 D228 H231 G233 G234 E235 R237 N238 F239 G240 K241 H242 P243 T245 W247 Q250 T251 K252 G253 K255 T256 R257 S258 K260 R261 R269 R270

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6pc8, PDBe:6pc8, PDBj:6pc8
• PDBsum: 6pc8
• PubMed: 32968273
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)