Structure of PDB 8whx Chain G Binding Site BS01

Receptor Information

>8whx Chain G (length=209) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

TLKVDVKTPAGKTDGSVELPAELFDVEPNIALMHQVVTAQLAAKRQGTHS
TKTRGEVSGGGKKPYRQKGTGRARQGSTRAPQFTGGGTVHGPKPRDYSQR
TPKKMIAAALRGALSDRARNDRIHAVTELVEGQTPSTKSAKTFLGTLTEN
KKVLVVIGRTDEVGAKSVRNLPGVHVISPDQLNTYDVLNADDVVFSVEAL
NAYISANSK

Ligand information

>8whx Chain A (length=3020)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaacuggucaagugauugugcgccgauaauguagc
ggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugggu
aggggagcguccugcauccggugaagccgccgagugaucgagugguggag
ggugugggagugagaaugcaggcaugaguagcgauuaggcaagugagaac
cuugcccgccgaaagaccaaggguuccugggccaggccaguccgcccagg
gugagucgggaccuaaggcgaggccgacaggcguagucgauggacaacgg
guugauauucccguacccguguaugugcguccaugaugaaucagcgguac
uaaccauccggcugcaugggaccuucguugguaguagucaagcgaugggg
ugacgcaggaagguagccguaccggucagugguaauaccgggguaagccu
guagggagucagauagguaaauccgucuggcauauauccugagaggugau
gcauagccgagugaggcgaauucggugauccuaugcugccgagaaaagcc
ucuagcgaggacauacacggcccguaccccaaaccaacacagguggucag
guagagaauacuaaggcguacgagugaacuaugguuaaggaacucggcaa
aaugcccccguaacuucgggagaagggggacccacauggcguguaagccu
uuacggcccaagcgugaguggguggcacaaaccagugagaagcgacuguu
uacuaaaaacacagguccgugcgaagucgcaagacgauguauacggacug
acgccugcccggugcuggaagguuaagaggacccguuaacucccuuuggg
ggugaagcggagaauuuaagccccaguaaacggcggugguaacuauaacc
auccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaau
ggcguaacgacuucucaacugucucaaccauagacucggcgaaauugcac
uacgaguaaagaugcucguuacgcgcggcaggacgaaaagaccccgggac
cuucacuacaacuugguauuggugcucgauacgguuuguguaggauaggu
gggagacugugaagcucacacgccaguguggguggagucguuguugaaau
accacucugaucguauugggccucuaaccucggaccguauauccgguuca
gggacagugccugguggguaguuuaacuggggcgguugccuccuaaaaug
uaacggaggcgcccaaagguucccucaaccuggacggcaaucagguguug
aguguaagugcacaagggagcuugacugcgagacggacaugucgagcagg
gacgaaagucgggacuagugauccggcaccucugaguggaaggggugucg
cucaacggauaaaagguaccccggggauaacaggcugaucuuccccaaga
gaucgacgggaugguuuggcaccucgaugucggcucgucgcauccugggg
cuggagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcg
agcuggguuuagaacgucgugagacaguucggucucuauccgccgcgcgc
gucagaagcuugaggaaaccugucccuaguacgagaggaccgggacggac
gaaccucugguauaccaguugucccaccaggggcacggcuggauagccac
guucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuuccaa
gaccaggcuucucacccucuaggagggauaaggccccccgcagaccacgg
gauugauagaccagaccuggaagccuaguaauaggugcagggaacuggca
cuaaccggccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8whx Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): H35 Q36 Q41 L42 K45 R46 Q47 T49 H50 S51 T52 K53 R55 G56 V58 S59 G60 K63 K64 Q68 K69 G70 G72 R73 A74 R75 G77 P82 Q83 T85 G86 V90 H91 P93 R96 Q100 R101 P103 K104 K105 M106 P136 S137 T138 K139 K142 K153 R160 K167 R170 N171 P173 H176 Q182 N184 Y186 D187
• Binding residue (residue number reindexed from 1): H34 Q35 Q40 L41 K44 R45 Q46 T48 H49 S50 T51 K52 R54 G55 V57 S58 G59 K62 K63 Q67 K68 G69 G71 R72 A73 R74 G76 P81 Q82 T84 G85 V89 H90 P92 R95 Q99 R100 P102 K103 K104 M105 P135 S136 T137 K138 K141 K152 R159 K166 R169 N170 P172 H175 Q181 N183 Y185 D186

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8whx, PDBe:8whx, PDBj:8whx
• PDBsum: 8whx
• PubMed: 38245551
• UniProt: A0QSD2|RL4_MYCS2 Large ribosomal subunit protein uL4 (Gene Name=rplD)