Structure of PDB 5wit Chain 2R Binding Site BS01

Receptor Information

>5wit Chain 2R (length=118) Species: 300852 (Thermus thermophilus HB8)

MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDH
LIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKL
AERRRGDGAPLALVELVE

Ligand information

>5wit Chain 2A (length=2800)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagccc
agcgccgaagcugcgggucuggggccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccgcgggugacaaccccccga
agccagggagccaagaaaagccucuaagcacaaccugcgggaacccguac
cgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggag
aacccucgccaaggaacucugcaaguuggccccguaacuucgggagaagg
ggugcucccuggggugaugagccccggggagccgcagugaacaggcucug
gcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggua
uagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaag
ccccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaa
cgaccggagcgcugucucggcgagggacccggugaaauugaacuggccgu
gaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuuac
ugcagccugguguuggcucuuggucgcgccugcguaggauaggugggagc
cugugaacccccgccuccgggugggggggaggcgccggugaaauaccacc
cuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaa
gguccccucaggcgggacggaaauccgccggagagcgcaaggguagaagg
gggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccua
gugaaccgguggucccguguggaagggccaucgaucaacggauaaaaguu
accccggggauaacaggcugaucucccccgagcguccacagcggcgggga
gguuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguc
ccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucag
aacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuug
aggggggcucuuccuaguacgagaggaccggaagggacgcaccucugguu
ucccagcugucccuccaggggcauaagcuggguagccaugugcggaaggg
auaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuc
ccggcagccgguaaggacccgggaagaccacccgguggaugggccggggg
uguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wit Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 S15 H16 R17 R22 N23 H31 I34 T35 T36 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 V73 R77 R90 Q91 G92 G93 T95 R96 K99 R104 R105 G106 D107 V117
• Binding residue (residue number reindexed from 1): M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 S15 H16 R17 R22 N23 H31 I34 T35 T36 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 L67 R68 Q71 V73 R77 R90 Q91 G92 G93 T95 R96 K99 R104 R105 G106 D107 V117

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5wit, PDBe:5wit, PDBj:5wit
• PDBsum: 5wit
• PubMed: 28934499
• UniProt: Q9Z9H5|RL17_THET8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)