Structure of PDB 4v9k Chain BW Binding Site BS01

Receptor Information

>4v9k Chain BW (length=113) Species: 262724 (Thermus thermophilus HB27)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHGK

Ligand information

>4v9k Chain BA (length=2879)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguuggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccc
aggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggc
ggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagg
gugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguc
agcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaag
ggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgc
ucuaggcuagggggaccggagccauggacgagcccggccagaagcgcagg
gugggagguaggcaaauccgccucccaaaagcucugcgugguggggaagc
ccguacgggugacaaccccccgaagccagggagccaagaaaagccucuaa
gcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugc
aagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguu
ggccccguaacuucgggagaaggggugcucccuggggugaugagcuccgg
ggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucu
cugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgg
aaggucaaggggaggggugcaagccccgaaccgaagccccggugaacggc
ggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggga
cccggugaaauugaacuggccgugaagaugcggccuacccguggcaggac
gaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgc
gccugcguaggauaggugggagccugugaacccccgccuccggguggggg
ggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucg
gauggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccu
aaaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccg
ccggagagcgcaaggguagaagggggccugacugcgaggccugcaagccg
agcaggggcgaaagccgggccuagugaaccgguggucccguguggaaggg
ccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccc
ccgagcguccacagcggcggggagguuuggcaccucgaugucggcucguc
gcauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaa
agcggcacgcgagcuggguucagaacgucgugagacaguucggucucuau
ccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagga
ccggaagggacgcaccucugguuucccagcugucccuccaggggcauaag
cuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggga
agcccgccccaagaugaggccucccacggcgucaagccgguaaggacccg
ggaagacuacccgguggaugggccggggguguaagcgccgcgaggcguug
agccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v9k Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K4 I6 A7 R8 S13 R15 K16 R18 R25 K41 R42 Y45 K49 S53 A56 N57 N61 D77 E78 G79 P80 L82 R84 P87 R88 A89 G91 R92 A93 D94 I95 I96 K97 K98 R99
• Binding residue (residue number reindexed from 1): K4 I6 A7 R8 S13 R15 K16 R18 R25 K41 R42 Y45 K49 S53 A56 N57 N61 D77 E78 G79 P80 L82 R84 P87 R88 A89 G91 R92 A93 D94 I95 I96 K97 K98 R99

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:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v9k, PDBe:4v9k, PDBj:4v9k
• PDBsum: 4v9k
• PubMed: 23812722
• UniProt: Q72I09|RL22_THET2 Large ribosomal subunit protein uL22 (Gene Name=rplV)