Structure of PDB 4v5a Chain BN Binding Site BS01

Receptor Information

>4v5a Chain BN (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4v5a Chain BA (length=2767)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccaagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcgccuacc
aaacccugucaaacuccgaagggucccagguggagccugggagugagggc
gcgagcgauaacguccgcguccgagcgcgggaacaaccgagaccgccagc
uaaggcccccaagucugggcuaagugguaaaggauguggcgccgcgaaga
cagccagucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucugggggaugaccccaggcgguaggggagcguucc
cgaugccgaugaaggccgacccgcgagggcggcuggagguaagggaagug
cgaaugccggcaugaguaacgauaaagagggugagaaucccucucgccgu
aagcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggac
cuaaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccg
gcccuucccgcaggugcgauggggggacgcucuaggcuagggggaccgga
gccauggacgagcccggccagaagcgcagggugggagguaggcaaauccg
ccucccaacaagcucugcgugguggggaagcccgcaaccccccgaagcca
gggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaa
accgacacaggugggcgggugcaagagcacucaggcgcgcgggagaaccc
ucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugc
ucccuggggugaugagccccggggagccgcagugaacaggcucuggcgac
uguuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggg
agcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccg
aaccgaagccccggugaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgccugcguaggauaggugggagcccggu
gaaauaccacccuggcgcggcugggggccuaacccucggauggggggaca
gcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacgg
aggcgcccaaagguccccucaggcgggacggaaauccgccggagagcgca
aggguagaagggggccugacugcgaggccugcaagccgagcaggggcgaa
agccgggccuagugaaccgguggucccguguggaagggccaucgaucaac
ggauaaaaguuaccccggggauaacaggcugaucucccccgagcguccac
agcggcggggagguuuggcaccucgaugucggcucgucgcauccuggggc
ugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcga
gcuggguucagaacgucgugagacaguucggucucuauccgccacgggcg
caggaggcuugaggggggcucuuccuaguacgagaggaccggaagggacg
caccucugguuucccagcugucccuccaggggcauaagcuggguagccau
gugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaa
gaugaggccucccacggcgucaagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5a Crystal structure of the ribosome recycling factor bound to the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K2 Y4 V5 W13 T22 R25 T28 R35 K37 N45 F51 T63 Q69 K70 T73 Y75 S76 G80 L82 K83 R97 H101 A102 G105 M106 L107 P108 K109 G110 P111 R114 K118 H130
• Binding residue (residue number reindexed from 1): K2 Y4 V5 W13 T22 R25 T28 R35 K37 N45 F51 T63 Q69 K70 T73 Y75 S76 G80 L82 K83 R97 H101 A102 G105 M106 L107 P108 K109 G110 P111 R114 K118 H130

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v5a, PDBe:4v5a, PDBj:4v5a
• PDBsum: 4v5a
• PubMed: 17660830
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)