Structure of PDB 4v9h Chain BQ Binding Site BS01

Receptor Information

>4v9h Chain BQ (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>4v9h Chain BA (length=2859)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccaagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccaggagguggcuuagaagcagccauccuuuaaagagugcg
uaauagcucacuggucgaguggcgccgcgccgaaaaugaucggggcuuaa
gcccagcgccgaagcugcgggucugggggaugaccccaggcgguagggga
gcguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaag
ggaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccuc
ucgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuag
gcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaa
uauuccggcccuucccgcaggugcgauggggggacgcucuaggcuagggg
gaccggagccauggacgagcccggccagaagcgcagggugggagguaggc
aaauccgccucccaacaagcucugcgugguggggaagcccggugacaacc
ccccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaac
ccguaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcg
cgggagaacccucgccaaggaacucugcaaguuggccccguaacuucggg
agaaggggugcucccuggggugaugagccccggggagccgcagugaacag
gcucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagag
gagguauagggagcgacgcuugcccggugccggaaggucaaggggagggg
ugcaagccccgaaccgaagccccggugaacggcggcguaacuauaacggu
ccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaag
cguaacgaccggagcgcugucucggcgagggacccggugaaauugaacug
gccgugaagaugcggccuacccguggcaggacgaaaagaccccguggagc
uuuacugcagccugguguuggcucuuggucgcgccugcguaggauaggug
ggagccugugaacccccgccuccgggugggggggaggcgccggugaaaua
ccacccuggcgcggcugggggccuaacccucggauggggggacagcgcuu
ggcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgc
ccaaagguccccucaggcgggacggaaauccgccggagagcgcaagggua
gaagggggccugacugcgaggccugcaagccgagcaggggcgaaagccgg
gccuagugaaccgguggucccguguggaagggccaucgaucaacggauaa
aaguuaccccggggauaacaggcugaucucccccgagcguccacagcggc
ggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaaga
aggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggg
uucagaacgucgugagacaguucggucucuauccgccacgggcgcaggag
gcuugaggggggcucuuccuaguacgagaggaccggaagggacgcaccuc
ugguuucccagcugucccuccaggggcauaagcuggguagccaugugcgg
aagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugag
gccucccacggcgaagccgguaaggacccgggaagaccacccgguggaug
ggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgu
ccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v9h Elongation factor G bound to the ribosome in an intermediate state of translocation.
• Resolution: 2.857 Å
• Binding residue (original residue number in PDB): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 Y26 F29 W41 Q46 A49 R56 R59 K63 R67 F69 D71 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128
• Binding residue (residue number reindexed from 1): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 Y26 F29 W41 Q46 A49 R56 R59 K63 R67 F69 D71 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:4v9h, PDBe:4v9h, PDBj:4v9h
• PDBsum: 4v9h
• PubMed: 23812720
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)