Structure of PDB 4v7m Chain DU Binding Site BS01

Receptor Information

>4v7m Chain DU (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

Ligand information

>4v7m Chain DA (length=2775)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucgccgaaucccc
agccuagccgaagcuguugggaagcagcgccagagagggugaaagccccg
uaggcgaaagguggggggauaggugaggguacccgaguaccccgugguuc
guggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacuc
cgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaaccc
cgggaggggagugaaauagagccugaaaccgugggcuuacaagcagucac
ggccccgggguuguggcgugccuauugaagcaugagccggcgacucacgg
ucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagucc
gaacagggcgguccgcggccguggacccgaaaccgggcgagcuagcccug
gccagggugaagcuggggugagacccaguggaggcccgaaccgguggggg
augcaaaccccucggaugagcuggggcuaggagugaaaagcuaaccgagc
ccggagauagcugguucuccccgaaaugacuuuagggucagccucaggcg
cugacuggggccuguagagcacugauagggcuagggggcccaccagccua
ccaaacccugucaaacuccgaagggucccagguggagccugggagugagg
gcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagaccgcca
gcuaaggcccccaagucugggcuaagugguaaaggauguggcgccgcggu
ggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgg
gucuggggccccaggcgguaggggagcguucccgaugccgaugaaggccg
acccgcgagggcggcuggagguaagggaagugcgaaugccggcaugagua
acgauaaagagggugagaaucccucucgccguaagcccaaggguuccuac
gcaauggucgucagcguaggguuaggcgggaccuaaggugaagccgaaag
gcguagccgaagggcagccgguuaauauuccggcccuucccgcaggugcg
auggggggacgcucuaggcuagggggaccggagccauggacgagcccggc
cagaagcgcagggugggagguaggcaaauccgccucccaacaagcucugc
gugguggggaagcaaccccccgaagccagggagccaagaaaagccucuaa
gcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugc
aagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguu
ggccccguaacuucgggagaaggggugcucccuggggugaugagccccgg
ggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucu
cugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgg
aaggucaaggggaggggugcaagccccgaaccgaagccccggugaacggc
ggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggga
cccggugaaauugaacuggccgugaagaugcggccuacccguggcaggac
gaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgc
gccugcguaggauaggugggagccugugaacccccgccuccggguggggg
ggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucg
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcgucaagccgguaaggacccgggaa
gaccacccgguggaugggccggggguguaagcgccgcgaggcguugagcc
gaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v7m The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 R10 R11 R12 K13 H14 K16 K19 K22 G23 Y24 W25 G26 L27 R28 K30 S31 R33 K34 R36 E37 A42 Y45 A46 Y47 A48 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 I62 N66 R70 N75 Y76 S77 H81 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 R9 R10 R11 K12 H13 K15 K18 K21 G22 Y23 W24 G25 L26 R27 K29 S30 R32 K33 R35 E36 A41 Y44 A45 Y46 A47 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 I61 N65 R69 N74 Y75 S76 H80 R91 K92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v7m, PDBe:4v7m, PDBj:4v7m
• PDBsum: 4v7m
• PubMed: 20154709
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)