Structure of PDB 4wce Chain A Binding Site BS01

Receptor Information

>4wce Chain A (length=269) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVR
HHGGGHKRQYRVIDFKRNKDGINAKVDSIQYDPNRSANIALVVYADGEKR
YIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGG
QIARSAGASAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHEL
VNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRPSPMSPWGK
PTLGKKTRRGKKSSDKLIV

Ligand information

>4wce Chain X (length=2708)

gauuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaau
gaaggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuu
gauccagagauuuccgaauggggaaacccagcaugaguuaugucauguua
ucgauauguauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaag
augaaucaaagaagguaauaauccuguagucgaaaauguugucucucuug
aguggauccugaguacgacggagcacgugaaauuccgucggaaucuggga
ggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagu
accgugagggaaaggugaaaagcaccccggaaggggagugaaauagaacc
ugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgu
gccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagca
guaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauu
uggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuc
aggcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaa
cugaggguagcggagaaauuccaaucgaaccuggagauagcugguucucu
ccgaaauagcuuuagggcuagccucaagugaugauuauuggagguagagc
acuguuuggacgaggguuaccgaauucagacaaacuccgaaugccaauua
auuuaacuugggagucagaacaugggugauaagguccguguucgaaaggg
aaacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaa
aggauguggcguugcccagacaacuagcucacuagucgagugacacugcg
ccgaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccuu
ggacaaugguaggagagcguucuaagggcguugaagcaugaucguaagga
cauguggagcgcuuagaagugagaaugccggugugaguagcgaaagacgg
gugagaaucccguccaccgauugacuaagguuuccagaggaaggcucguc
cgcucuggguuagucggguccuaagcugaggccgacaggcguaggcgaug
gauaacagguugauauuccuguaccaccuauaaucguaucgaugggggga
cgcaguaggauaggcgaagcgugcgauuggauugcacgucuaagcaguag
gcgaguaauccgguacucgggcugagcugugauggggagaagagagucgu
ugauuucacacugccgagaaaagccucuagauagaauaggugcccguacc
gcaaaccgacacagguagucaagaugagaauucuaaggugagcgagcgaa
cucucguuaaggaacucggcaaaaugaccccguaacuucgggagaagggg
ugcucuuuaggguuaacgcccagaagagccgcagugaauaggcccaagcg
acuguuuaucaaaaacacaggucucugcuaaaccguaaggugauguauag
gggcugacgccugcccgugcuggaagguuaagaggagugguuagcugcga
agcuacgaaucgaagccccaguaaacggcggcuaagguagcgaaauuccu
ugucggguaaguuccgacccgcacgaaaggcguaacgauuugggcacugu
cucaacgagagacucggugaaaucauaguaccugugaagaugcagguuac
ccgcgacaggacggaaagaccccguggagcuuuacuguagccugauauug
aaauucggcuuucuaacccgcaccacuuaucguggugggagacaguguca
agcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgc
ucaaagguucccucagaaugguugaaaucauucauagaguguaaaggcau
aagggagcuugacugcgagaccuacaagucgagcagggucgaaagacgga
cuuagugauccggugguuccgcauggaagggccaucgcucaacggauaaa
agcuaccccggggauaacaggcuuaucucccccaagaguucacaucgacg
gggagguuuggcaccucgaugucggcucaucgcauccuggggcuguaguc
ggucccaaggguugggcuguucgcccauuaaagcgguacgcgagcugggu
ucagaacgucgugagacaguucggucccuauccgucgugggcguaggaaa
uuugagaggagcuguccuuaguacgagaggaccgggauggacauaccucu
gguguaccaguugucgugccaacggcauagcuggguagcuauguguggac
gggauaagugcugaaagcaucuaagcaugaagccccccucaagaugagau
uucccaacuugguuauaagaucccucaaagaugaugagguuaauagguuc
gagguggaagcauggugacauguggagcugacgaauacuaaucgaucgaa
gacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wce Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
• Resolution: 3.526 Å
• Binding residue (original residue number in PDB): P8 I9 T10 N11 G12 R14 K40 A41 R43 N44 N45 Q46 G47 K48 L49 T50 V51 H53 H54 G56 H58 K59 R60 Q61 P85 V95 D98 G99 G149 Q153 I154 A155 R156 S157 A158 G159 Y171 L176 S178 E180 L198 H200 E201 N204 V205 G206 A208 R210 S211 R212 W213 R217 P218 T219 V220 R221 G222 S223 V224 M225 N226 P227 N228 D229 H232 G234 G235 E236 G237 R238 P240 I241 G242 R243 P244 P246 S248 P249 W250 T254 G256 K258 T259 R260 S266
• Binding residue (residue number reindexed from 1): P6 I7 T8 N9 G10 R12 K38 A39 R41 N42 N43 Q44 G45 K46 L47 T48 V49 H51 H52 G54 H56 K57 R58 Q59 P83 V93 D96 G97 G147 Q151 I152 A153 R154 S155 A156 G157 Y169 L174 S176 E178 L196 H198 E199 N202 V203 G204 A206 R208 S209 R210 W211 R215 P216 T217 V218 R219 G220 S221 V222 M223 N224 P225 N226 D227 H230 G232 G233 E234 G235 R236 P238 I239 G240 R241 P242 P244 S246 P247 W248 T252 G254 K256 T257 R258 S264

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4wce, PDBe:4wce, PDBj:4wce
• PDBsum: 4wce
• PubMed: 26464510
• UniProt: P60430|RL2_STAA8 Large ribosomal subunit protein uL2 (Gene Name=rplB)