Structure of PDB 4v7l Chain DR Binding Site BS01

Receptor Information

>4v7l Chain DR (length=117) Species: 300852 (Thermus thermophilus HB8)

RHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHL
IHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLA
ERRRGDGAPLALVELVE

Ligand information

>4v7l Chain DA (length=2800)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccaagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgguccgcggccguggacccgaaaccgggcgagcuagcc
cuggccagggugaagcuggggugagacccaguggaggcccgaaccggugg
gggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaaccg
agcccggagauagcugguucuccccgaaaugacuuuagggucagccucag
gcgcugacuggggccuguagagcacugauagggcuagggggcccaccagc
cuaccaaacccugucaaacuccgaagggucccagguggagccugggagug
agggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagaccg
ccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccgc
gaagacagccagucgaguggcgccgcgccgaaaaugaucggggcuuaagc
ccagcgccgaagcugcgggucugggggaugaccccaggcgguaggggagc
guucccgaugccgaugaaggccgacccgcgagggcggcuggagguaaggg
aagugcgaaugccggcaugaguaacgauaaagagggugagaaucccucuc
gccguaagcccaaggguuccuacgcaauggucgucagcguaggguuaggc
gggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaaua
uuccggcccuucccgcaggugcgauggggggacgcucuaggcuaggggga
ccggagccauggacgagcccggccagaagcgcagggugggagguaggcaa
auccgccucccaacaagcucugcgugguggggaaaaccccccgaagccag
ggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaaa
ccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaacccu
cgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugcu
cccuggggugaugagccccggggagccgcagugaacaggcucuggcgacu
guuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggga
gcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccga
accgaagccccggugaacggcggccguaacuauaacgguccuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgaccg
gagcgcugucucggcgagggacccggugaaauugaacuggccgugaagau
gcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcagc
cugguguuggcucuuggucgcgccugcguaggauaggugggagccuguga
acccccgccuccgggugggggggaggcgccggugaaauaccacccuggcg
cggcugggggccuaacccucggauggggggacagcgcuuggcgggcaguu
ugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagguccc
cucaggcgggacggaaauccgccggagagcgcaaggguagaagggggccu
gacugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaac
cgguggucccguguggaagggccaucgaucaacggauaaaaguuaccccg
gggauaacaggcugaucucccccgagcguccacagcggcggggagguuug
gcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaagg
guugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacguc
gugagacaguucggucucuauccgccacgggcgcaggaggcuugaggggg
gcucuuccuaguacgagaggaccggaagggacgcaccucugguuucccag
cugucccuccaggggcauaagcuggguagccaugugcggaagggauaacc
gcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacgg
cgucaagccgguaaggacccgggaagaccacccgguggaugggccggggg
uguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v7l The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R2 H3 L4 K5 S6 G7 R8 K9 L10 N11 H13 S14 S15 H16 N23 Q24 S27 H31 I34 T35 T36 T37 P39 K40 K42 R45 G46 D49 H50 H53 R57 H61 R64 L67 R68 Q71 R77 R90 Q91 G92 G93 R96 R104 R105 G106 D107 A109 V117
• Binding residue (residue number reindexed from 1): R1 H2 L3 K4 S5 G6 R7 K8 L9 N10 H12 S13 S14 H15 N22 Q23 S26 H30 I33 T34 T35 T36 P38 K39 K41 R44 G45 D48 H49 H52 R56 H60 R63 L66 R67 Q70 R76 R89 Q90 G91 G92 R95 R103 R104 G105 D106 A108 V116

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:4v7l, PDBe:4v7l, PDBj:4v7l
• PDBsum: 4v7l
• PubMed: 20154709
• UniProt: Q9Z9H5|RL17_THET8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)