Structure of PDB 5jvh Chain P Binding Site BS01

Receptor Information

>5jvh Chain P (length=127) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

FRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLL
RFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLI
PRARGSANIIKKRTSHITIIVAEKGNK

Ligand information

>5jvh Chain X (length=2658)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaac
ucaagccgaaguggcuggaaagcuacaccucagaaggugagaguccugua
ggcgaacgagcuaggucguuguucgugaaacgaugacugaauccgcgcgg
accaccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccg
ugagggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaa
accguggacuuacaagcagucauggcaccuuaugcguguuauggcgugcc
uauugaagcaugagccggcgacuuagaccugacgugcgagcuuaaguuga
aaaacggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgu
cgggcuagacucgaaaccaggugagcuaagcaugaccagguugaaacccc
cgugacagggggcggaggaccgaaccggugccugcugaaacagucucgga
ugaguuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguu
cuccccgaaauguauugagguacagccucggauguugaccauguccugua
gagcacucacaaggcuaaaccuuaugaaacuccgaaggggcacgcguuua
guccgggagugaggcugcgagagcuaacuuccguagccgagagggaaaca
acccagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggau
gugucgucgcauagacagcuggcuuagaagcaugcguaauagcucacugg
ucgagugacgaugcgccgaaaaugaucggggcucaagugaucuaccgaag
cuauggauucaacucgcgaagcgaguugucugguaggggagcguucaguc
cgcggagaagccauaccggaaggagugguggagccgacugaagugcggau
gccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaagga
caaggguuccuggggaagggucguccgcccagggaaagucgggaccuaag
gugaggccgaacggcgcagccgauggacagcaggucaagauuccugcacc
gaucauguggagugauggagggacgcauuacgcuauccaaugccaagcua
uggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuacc
ggucacaugccucagacguaucgggagcuuccucggaagcgaaguuggaa
acgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccgu
accgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcgag
agaacccucguuaaggaacuuugcaaucucaccccguaacuucggaagaa
gggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacugu
uuaccaaaaucacagcacucugccaacacgaacaguggacguauagggug
ugacgccugcccggugccggaaggucaaguggagcggugcaagcugcgaa
augaagccccggugaacggcuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaggcguaacgaucugggcgcugucucaacgaggga
cucggugaaauugaauuggcuguaaagaugcggccuacccguagcaggac
gaaaagaccccguggagcuuuacuauagucuggcauugggauucggguuu
cugaaacuuggauuucuaaccugaaaaaucacuuucggggaccgugcuug
gcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcc
caaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguag
aagguggcuugacugcgagacugacacgucgagcagggaggaaacucggg
cuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagaguccauaucggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggaga
auugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcu
ggucucccugcugucguaccaacggcacaugcaggguagcuauguccgga
acggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugagu
ucucccacugagguaagacucccggaagaccaccggguuaagaggccagg
cgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggu
cuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jvh Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
• Resolution: 3.58 Å
• Binding residue (original residue number in PDB): R9 K11 K12 R14 K15 Q16 V18 K19 L20 R21 K22 V27 A28 K29 Y30 R32 S34 R36 K37 R39 R62 S63 K70 N73 S74 A77 N78 H81 N82 Y96 D98 A99 P101 R105 P108 R109 A110 R111 G112 S113 A114 N115 I117 K118 K119 R120 H123
• Binding residue (residue number reindexed from 1): R2 K4 K5 R7 K8 Q9 V11 K12 L13 R14 K15 V20 A21 K22 Y23 R25 S27 R29 K30 R32 R55 S56 K63 N66 S67 A70 N71 H74 N75 Y89 D91 A92 P94 R98 P101 R102 A103 R104 G105 S106 A107 N108 I110 K111 K112 R113 H116

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

External links

• PDB: RCSB:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RXJ7|RL22_DEIRA Large ribosomal subunit protein uL22 (Gene Name=rplV)