Structure of PDB 4v51 Chain DN Binding Site BS01

Receptor Information

>4v51 Chain DN (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4v51 Chain DA (length=2772)

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
ccugguguuggcucuuggucgcgccugcguaggauaggugggagccuggc
gccggugaaauccacccuggcgcggcugggggccuaacccucggaugggg
ggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaaggu
aacggaggcgcccaaagguccccucaggcgggacggaaauccgccggaga
gcgcaaggguagaagggggccugacugcgaggccugcaagccgagcaggg
gcgaaagccgggccuagugaaccgguggucccguguggaagggccaucga
ucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagcg
uccacagcggcggggagguuuggcaccucgaugucggcucgucgcauccu
ggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggca
cgcgagcuggguucagaacgucgugagacaguucggucucuauccgccac
gggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaag
ggacgcaccucugguuucccagcugucccuccaggggcauaagcugggua
gccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgc
cccaagaugaggccucccacggcgucaagccgguaaggacccgggaagac
cacccgguggaugggccggggguguaagcgccgcgaggcguugagccgac
cggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v51 Structure of the 70S ribosome complexed with mRNA and tRNA.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y4 W13 T22 L23 R25 T28 N45 F51 T63 G64 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 K89 R97 A102 G105 M106 P108 G110 P111 L112 R114 R115 K118 H130
• Binding residue (residue number reindexed from 1): Y4 W13 T22 L23 R25 T28 N45 F51 T63 G64 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 K89 R97 A102 G105 M106 P108 G110 P111 L112 R114 R115 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:4v51, PDBe:4v51, PDBj:4v51
• PDBsum: 4v51
• PubMed: 16959973
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)