Structure of PDB 4v5c Chain BO Binding Site BS02

Receptor Information

>4v5c Chain BO (length=122) Species: 300852 (Thermus thermophilus HB8)

MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRG
AVKEGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFG
PVARELREKGFMKIVSLAPEVL

Ligand information

>4v5c Chain BA (length=2807)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccaagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccagucgaguggcgccgcgccgaaaaugaucggggcuuaag
cccagcgccgaagcugcgggucugggggaugaccccaggcgguaggggag
cguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaagg
gaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccucu
cgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuagg
cgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaau
auuccggcccuucccgcaggugcgauggggggacgcucuaggcuaggggg
accggagccauggacgagcccggccagaagcgcagggugggagguaggca
aauccgccucccaacaagcucugcgugguggggaagcccgcaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5c Insights Into Substrate Stabilization from Snapshots of the Peptidyl Transferase Center of the Intact 70S Ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): M1 Q3 Q5 T6 Y7 I22 R23 S28 N29 K31 Y32 V40 S42 K44 K67 E68 K70 R78
• Binding residue (residue number reindexed from 1): M1 Q3 Q5 T6 Y7 I22 R23 S28 N29 K31 Y32 V40 S42 K44 K67 E68 K70 R78

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit 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:4v5c, PDBe:4v5c, PDBj:4v5c
• PDBsum: 4v5c
• PubMed: 19363482
• UniProt: Q5SHP8|RL14_THET8 Large ribosomal subunit protein uL14 (Gene Name=rplN)