Structure of PDB 4v9s Chain BP Binding Site BS01

Receptor Information

>4v9s Chain BP (length=149) Species: 300852 (Thermus thermophilus HB8)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLE

Ligand information

>4v9s Chain BA (length=2731)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcagcggccgcaaaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagcggucgaguggcgccgcgccgaaaaugau
cggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccagg
cgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggc
uggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggug
agaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagc
guaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggc
agccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucu
aggcuagggggaccggagccauggacgagcccggccagaagcgcagggug
ggagguaggcaaauccgccucccaacaagcucugcgugguggggaagccc
gggugacaaccccccgaagccagggagccaagaaaagccucuaagcacaa
ccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagc
acucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcccc
guaacuucgggagaaggggugcucccuggggugaugagccccggggagcc
gcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcga
acucguaagaggagguauagggagcgacgcuugcccggugccggaagguc
aaggggaggggugcaagccccgaaccgaagccccggugaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccggu
gaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaag
accccguggagcuuuacugcagccugguguuggcucuugugggggccuaa
cccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucg
ccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgga
aauccgccggagagcgcaaggguagaagggggccugacugcgaggccugc
aagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugug
gaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcuga
ucucccccgagcguccacagcggcggggagguuuggcaccucgaugucgg
cucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgcc
cauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucggu
cucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacg
agaggaccggaagggacgcaccucugguuucccagcugucccuccagggg
cauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaa
gcgggaagcccgccccaagaugaggccucccacggcagccgguaaggacc
cgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcgu
ugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v9s The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): L3 S4 R7 P8 N9 P10 A12 N13 K14 R15 R16 K17 R18 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 P48 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 Q70 V71 P72 G73 E74 I75 K76 R77 Q81 N84 R90 K107 K108 K113 L115 G116 E117 S131 K132 S133
• Binding residue (residue number reindexed from 1): L3 S4 R7 P8 N9 P10 A12 N13 K14 R15 R16 K17 R18 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 P48 R50 F51 E52 G53 G54 R55 S56 M60 R61 P63 K64 R65 G66 M67 Q70 V71 P72 G73 E74 I75 K76 R77 Q81 N84 R90 K107 K108 K113 L115 G116 E117 S131 K132 S133

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v9s, PDBe:4v9s, PDBj:4v9s
• PDBsum: 4v9s
• PubMed: 24412368
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)