Structure of PDB 4v6a Chain DU Binding Site BS01

Receptor Information

>4v6a Chain DU (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

Ligand information

>4v6a Chain DA (length=2777)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccggggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcguccgcggccguggacccgaaaccgggcgag
cuagcccuggccagggugaagcuggggugagacccaguggaggcccgaac
cggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagc
uaaccgagcccggagauagcugguucuccccgaaaugacuuuagggucag
ccucaggcgcugacuggggccuguagagcacugauagggcuagggggccc
accagccuaccaaacccugucaaacuccgaagggucccagguggagccug
ggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccg
agaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugugg
cgccgcgaagacagccggucgaguggcgccgcgccgaaaaugaucggggc
uuaagcccagcgccgaagcugcgggucugggggaugaccccaggcgguag
gggagcguucccgaugccgaugaaggccgacccgcgagggcggcuggagg
uaagggaagugcgaaugccggcaugaguaacgauaaagagggugagaauc
ccucucgccguaagcccaaggguuccuacgcaauggucgucagcguaggg
uuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgg
uuaauauuccggcccuucccgcaggugcgauggggggacgcucuaggcua
gggggaccggagccauggacgagcccggccagaagcgcagggugggaggu
aggcaaauccgccucccaacaagcucugcgugguggggaagcccaacccc
ccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaaccc
guaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcg
ggagaacccucgccaaggaacucugcaaguuggccccguaacuucgggag
aaggggugcucccuggggugaugagccccggggagccgcagugaacaggc
ucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagagga
gguauagggagcgacgcuugcccggugccggaaggucaaggggaggggug
caagccccgaaccgaagccccggugaacggcggccguaacuauaacgguc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagc
guaacgaccggagcgcugucucggcgagggacccggugaaauugaacugg
ccgugaagaugcggccuacccguggcaggacgaaaagaccccguggagcu
uuacugcagccugguguuggcucuuggucgcgccugcguaggauaggugg
gagcgccggugaaauaccacccuggcgcggcugggggccuaacccucgga
uggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaa
aagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgcc
ggagagcgcaaggguagaagggggccugacugcgaggccugcaagccgag
caggggcgaaagccgggccuagugaaccgguggucccguguggaagggcc
aucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccccc
gagcguccacagcggcggggagguuuggcaccucgaugucggcucgucgc
auccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaag
cggcacgcgagcuggguucagaacgucgugagacaguucggucucuaucc
gccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggacc
ggaagggacgcaccucugguuucccagcugucccuccaggggcauaagcu
ggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaag
cccgccccaagaugaggccucccacggcgucaagccgguaaggacccggg
aagaccacccgguggaugggccggggguguaagcgccgcgaggcguugag
ccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6a Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 V8 V9 R10 R11 K13 H14 K15 K16 K22 G23 Y24 W25 G26 L27 R28 K30 S31 F32 R33 K34 R36 E37 A42 Y45 A46 Y47 H49 K51 R52 R53 K54 R55 F57 R59 I62 N66 R70 N75 Y76 S77 I80 H81 K84 R92 K93 N94
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 V7 V8 R9 R10 K12 H13 K14 K15 K21 G22 Y23 W24 G25 L26 R27 K29 S30 F31 R32 K33 R35 E36 A41 Y44 A45 Y46 H48 K50 R51 R52 K53 R54 F56 R58 I61 N65 R69 N74 Y75 S76 I79 H80 K83 R91 K92 N93

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6a, PDBe:4v6a, PDBj:4v6a
• PDBsum: 4v6a
• PubMed: 19696344
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)