Structure of PDB 5hkv Chain B Binding Site BS01

Receptor Information

>5hkv Chain B (length=215) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

TKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQV
GFEDKKAYKKDAKSNKYANKPAEGHAKKADAAPKRFIREFRNVDVDAYEV
GQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAP
GSVGMASDASRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNV
PGPKKGLVEIRTSIK

Ligand information

>5hkv Chain X (length=2695)

gauuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaau
gaaggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuu
gauccagagauuuccgaauggggaaacccagcaugaguuaugucauguua
ucgauauguauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaag
augaaucaaagaagguaauaauccuguagucgaaaauguugucucucuug
aguggauccugaguacgacggagcacgugaaauuccgucggaaucuggga
ggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagu
accgugagggaaaggugaaaagcaccccggaaggggagugaaauagaacc
ugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgu
gccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagca
guaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauu
uggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuc
aggcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaa
cugaggguagcggagaaauuccaaucgaaccuggagauagcugguucucu
ccgaaauagcuuuagggcuagccucaagugaugauuauuggagguagagc
acuguuuggacgaggguuaccgaauucagacaaacuccgaaugccaauua
auuuaacuugggagucagaacaugggugauaagguccguguucgaaaggg
aaacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaa
aggauguggcguugcccagacaacuaguagucgagugacacugcgccgaa
aauguaccggggcuaaacauauuaccgaagcuguggauugucuggacaau
gguaggagagcguucuaagggcguugaagcaugaucguaaggacaugugg
agcgcuuagaagugagaaugccggugugaguagcgaaagacgggugagaa
ucccguccaccgauugacuaagguuuccagaggaaggcucguccgcucug
gguuagucggguccuaagcugaggccgacaggcguaggcgauggauaaca
gguugauauuccuguaccaccuauaaucguaucgauggggggacgcagua
ggauaggcgaagcgugcgauuggauugcacgucuaagcaguaggcgagua
auccgguacucgggcugagcugugauggggagaagagagucguugauuuc
acacugccgagaaaagccucuagauagaauaggugcccguaccgcaaacc
gacacagguagucaagaugagaauucuaaggugagcgagcgaacucucgu
uaaggaacucggcaaaaugaccccguaacuucgggagaaggggugcucuu
uaggguuaacgcccagaagagccgcagugaauaggcccaagcgacuguuu
aucaaaaacacaggucucugcuaaaccguaaggugauguauaggggcuga
cgccugcccgugcuggaagguuaagaggagugguuagcugcgaagcuacg
aaucgaagccccaguaaacggcgcuaagguagcgaaauuccuugucgggu
aaguuccgacccgcacgaaaggcguaacgauuugggcacugucucaacga
gagacucggugaaaucauaguaccugugaagaugcagguuacccgcgaca
ggacggaaagaccccguggagcuuuacuguagccugauauugaaauucgg
cuuucuaacccgcaccacuuaucgugugggagacagugucaagcgggcag
uuugacuggggcggucgccuccuaaaagguaacggaggcgcucaaagguu
cccucagaaugguuucauucauagaguguaaaggcauaagggagcuugac
ugcgagaccuacaagucgagcagggucgaaagacggacuuagugauccgg
ugguuccgcauggaagggccaucgcucaacggauaaaagcuaccccgggg
auaacaggcuuaucucccccaagaguucacaucgacggggagguuuggca
ccucgaugucggcucaucgcauccuggggcuguagucggucccaaggguu
gggcuguucgcccauuaaagcgguacgcgagcuggguucagaacgucgug
agacaguucggucccuauccgucgugggcguaggaaauuugagaggagcu
guccuuaguacgagaggaccgggauggacauaccucugguguaccaguug
ucgugccaacggcauagcuggguagcuauguguggacgggauaagugcug
aaagcaucuaagcaugaagccccccucaagaugagauuucccaacuuggu
uauaagaucccucaaagaugaugagguuaauagguucgagguggaagcau
ggugacauguggagcugacgaauacuaaucgaucgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hkv Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
• Resolution: 3.66 Å
• Binding residue (original residue number in PDB): M12 Q14 P24 D44 Y46 K64 S65 N66 K67 Y68 N70 K71 P72 G75 H76 R86 I88 E90 R92 S122 K123 G124 K125 F127 Q128 G129 K132 R133 Q136 S137 R138 M141 S142 H143 G144 S145 H146 F147 H148 R149 G152 S153 V154 M156 A157 S158 D159 A160 S161 R162 V163 F164 K165 Q167 M169 P170 R172 T177 T179 Q181 N182 L183 N200 V201 P202 K206 K216
• Binding residue (residue number reindexed from 1): M11 Q13 P23 D43 Y45 K63 S64 N65 K66 Y67 N69 K70 P71 G74 H75 R85 I87 E89 R91 S121 K122 G123 K124 F126 Q127 G128 K131 R132 Q135 S136 R137 M140 S141 H142 G143 S144 H145 F146 H147 R148 G151 S152 V153 M155 A156 S157 D158 A159 S160 R161 V162 F163 K164 Q166 M168 P169 R171 T176 T178 Q180 N181 L182 N199 V200 P201 K205 K215

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:5hkv, PDBe:5hkv, PDBj:5hkv
• PDBsum: 5hkv
• PubMed: 28973455
• UniProt: Q2FW06|RL3_STAA8 Large ribosomal subunit protein uL3 (Gene Name=rplC)