Structure of PDB 4v9h Chain B8 Binding Site BS01

Receptor Information

>4v9h Chain B8 (length=63) Species: 300852 (Thermus thermophilus HB8)

PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPY

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): P2 K3 M4 K5 T6 H7 K8 K11 K12 R13 K15 T17 A18 S19 K26 T27 G28 K29 R30 H31 L32 N33 W34 Q35 K39 I41 R42 Q43 R46 F48 V49 K52 L62 Y64
• Binding residue (residue number reindexed from 1): P1 K2 M3 K4 T5 H6 K7 K10 K11 R12 K14 T16 A17 S18 K25 T26 G27 K28 R29 H30 L31 N32 W33 Q34 K38 I40 R41 Q42 R45 F47 V48 K51 L61 Y63

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:4v9h, PDBe:4v9h, PDBj:4v9h
• PDBsum: 4v9h
• PubMed: 23812720
• UniProt: Q5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)