Structure of PDB 4v6a Chain DQ Binding Site BS01

Receptor Information

>4v6a Chain DQ (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

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): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 F29 R56 R67 D71 Y74 K77 L79 E80 R82 M83 G84 K85 G86 K87 R101 R119 I120 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 F29 R56 R67 D71 Y74 K77 L79 E80 R82 M83 G84 K85 G86 K87 R101 R119 I120 H123 K124 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:4v6a, PDBe:4v6a, PDBj:4v6a
• PDBsum: 4v6a
• PubMed: 19696344
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)