Structure of PDB 5jvh Chain B Binding Site BS01

Receptor Information

>5jvh Chain B (length=205) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIG
YAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGE
KIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRV
YKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRS
AAKAS

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): M11 T12 P22 Q35 D42 Y44 Q48 R57 K58 N60 K61 P62 M63 G65 H66 K69 R76 R79 E80 R82 S108 K109 G110 K111 G112 T113 Q114 G115 M117 K118 R119 N121 F122 A123 A127 S128 H129 G130 S131 K132 K133 W134 R136 R137 P138 G139 S140 I141 G142 Q143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 R155 M156 A157 H159 M162 R164 T166 Q168 N169 G186 A187 I188 P189 G190 A191 N192 K203
• Binding residue (residue number reindexed from 1): M11 T12 P22 Q35 D42 Y44 Q48 R57 K58 N60 K61 P62 M63 G65 H66 K69 R76 R79 E80 R82 S108 K109 G110 K111 G112 T113 Q114 G115 M117 K118 R119 N121 F122 A123 A127 S128 H129 G130 S131 K132 K133 W134 R136 R137 P138 G139 S140 I141 G142 Q143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 R155 M156 A157 H159 M162 R164 T166 Q168 N169 G186 A187 I188 P189 G190 A191 N192 K203

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:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RXK2|RL3_DEIRA Large ribosomal subunit protein uL3 (Gene Name=rplC)