Structure of PDB 4v63 Chain D6 Binding Site BS01

Receptor Information

>4v63 Chain D6 (length=44) Species: 262724 (Thermus thermophilus HB27)

LLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREV

Ligand information

>4v63 Chain DA (length=2879)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguuggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccc
aggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggc
ggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagg
gugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguc
agcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaag
ggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgc
ucuaggcuagggggaccggagccauggacgagcccggccagaagcgcagg
gugggagguaggcaaauccgccucccaaaagcucugcgugguggggaagc
ccguacgggugacaaccccccgaagccagggagccaagaaaagccucuaa
gcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugc
aagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguu
ggccccguaacuucgggagaaggggugcucccuggggugaugagcuccgg
ggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucu
cugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgg
aaggucaaggggaggggugcaagccccgaaccgaagccccggugaacggc
ggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggga
cccggugaaauugaacuggccgugaagaugcggccuacccguggcaggac
gaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgc
gccugcguaggauaggugggagccugugaacccccgccuccggguggggg
ggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucg
gauggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccu
aaaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccg
ccggagagcgcaaggguagaagggggccugacugcgaggccugcaagccg
agcaggggcgaaagccgggccuagugaaccgguggucccguguggaaggg
ccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccc
ccgagcguccacagcggcggggagguuuggcaccucgaugucggcucguc
gcauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaa
agcggcacgcgagcuggguucagaacgucgugagacaguucggucucuau
ccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagga
ccggaagggacgcaccucugguuucccagcugucccuccaggggcauaag
cuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggga
agcccgccccaagaugaggccucccacggcgucaagccgguaaggacccg
ggaagacuacccgguggaugggccggggguguaagcgccgcgaggcguug
agccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v63 Structural basis for translation termination on the 70S ribosome
• Resolution: 3.207 Å
• Binding residue (original residue number in PDB): R19 Y21 T23 E24 K25 K27 T30 E35 R37 Y39 W42 K45 H46
• Binding residue (residue number reindexed from 1): R11 Y13 T15 E16 K17 K19 T22 E27 R29 Y31 W34 K37 H38

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v63, PDBe:4v63, PDBj:4v63
• PDBsum: 4v63
• PubMed: 18596689
• UniProt: Q72GW3|RL33_THET2 Large ribosomal subunit protein bL33 (Gene Name=rpmG)