Structure of PDB 4v6g Chain DO Binding Site BS01

Receptor Information

>4v6g Chain DO (length=150) Species: 300852 (Thermus thermophilus HB8)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Ligand information

>4v6g Chain DA (length=2886)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgcaaacgaaaaguccgcggccguggaccc
gaaaccgggcgagcuagcccuggccagggugaagcuggggugagacccag
uggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcu
aggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaug
acuuuagggucagccucaggcgcugacuggggccuguagagcacugauag
ggcuagggggcccaccagccuaccaaacccugucaaacuccgaagggucc
cagguggagccugggagugagggcgcgagcgauaacguccgcguccgagc
gcgggaacaaccgagaccgccagcuaaggcccccaagucugggcuaagug
guaaaggauguggcgccgcgaagacagccaggauguuggcuuagaagcag
ccaucauuuaaagagugcguaauagcucacuggucgaguggcgccgcgcc
gaaaaugaucggggcuuaagcccagcgccgaagcugcgggucugggggau
gaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccgc
gagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgaua
aagagggugagaaucccucucgccguaagcccaaggguuccuacgcaaug
gucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguag
ccgaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggg
ggacgcucuaggcuagggggaccggagccauggacgagcccggccagaag
cgcagggugggagguaggcaaauccgccucccaacaagcucugcguggug
gggaagcccguacgggugacaaccccccgaagccagggagccaagaaaag
ccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagguggg
cgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucu
gcaaguuggccccguaacuucgggagaaggggugcucccuggggugauga
gccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaaca
cagcucucugcgaacucguaagaggagguauagggagcgacgcuugcccg
gugccggaaggucaaggggaggggugcaagccccgaaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucgg
cgagggacccggugaaauugaacuggccgugaagaugcggccuacccgug
gcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcucu
uggucgcgccugcguaggauaggugggagccugugaacccccgccuccgg
gugggggggaggcgccggugaaauaccacccuggcgcggcugggggccua
acccucggauggggggacagcgcuuggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgg
aaauccgccggagagcgcaaggguagaagggggccugacugcgaggccug
caagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugu
ggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcug
aucucccccgagcguccacagcggcggggagguuuggcaccucgaugucg
gcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgc
ccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgg
ucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguac
gagaggaccggaagggacgcaccucugguuucccagcugucccuccaggg
gcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucua
agcgggaagcccgccccaagaugaggccucccacggcgucaagccgguaa
ggacccgggaagaccacccgguggaugggccggggguguaagcgccgcga
ggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6g Structural aspects of messenger RNA reading frame maintenance by the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): L3 S4 R7 P8 N9 G11 N13 K14 R15 K17 R18 G20 R21 G22 P23 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 K46 R49 R50 F51 E52 G53 G54 R55 S56 L59 M60 R61 L62 P63 K64 G66 M67 Q70 V71 P72 G73 E74 I75 K76 R77 N84 G104 K107 K108 K113 L115 G116 E117 S131 K132 S133 A150
• Binding residue (residue number reindexed from 1): L3 S4 R7 P8 N9 G11 N13 K14 R15 K17 R18 G20 R21 G22 P23 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 K46 R49 R50 F51 E52 G53 G54 R55 S56 L59 M60 R61 L62 P63 K64 G66 M67 Q70 V71 P72 G73 E74 I75 K76 R77 N84 G104 K107 K108 K113 L115 G116 E117 S131 K132 S133 A150

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:4v6g, PDBe:4v6g, PDBj:4v6g
• PDBsum: 4v6g
• PubMed: 20400952
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)