Structure of PDB 4v5e Chain DE Binding Site BS01

Receptor Information

>4v5e Chain DE (length=204) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

Ligand information

>4v5e Chain DA (length=2886)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcaagggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguccgcggc
cguggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggu
gagacccaguggaggcccgaaccggugggggaugcaaaccccucggauga
gcuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucuc
cccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagag
cacugauagggcuagggggcccaccagccuaccaaacccugucaaacucc
gaagggucccagguggagccugggagugagggcgcgagcgauaacguccg
cguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucug
ggcuaagugguaaaggauguggcgcggcgaagacagccaggagguuggcu
uagaagcagccauccuuuaaagagugcguaauagcucacuggucgagucg
cgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggu
cugggggaugaccccaggcgguaggggagcguucccgaugccgaugaagg
ccgacccgcgagggcggcuggagguaagggaagugcgaaugccggcauga
guaacgauaaagagggugagaaucccucucgccguaagcccaaggguucc
uacgcaauggucgucagcguaggguuaggcgggaccuaaggugaagccga
aaggcguagccgaagggcagccgguuaauauuccggcccuucccgcaggu
gcgauggggggacgcucuaggcuagggggaccggagccauggacgagccc
ggccagaagcgcagggugggagguaggcaaauccgccucccaacaagcuc
ugcgugguggggaagcccgcaaccccccgaagccagggagccaagaaaag
ccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagguggg
cgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucu
gcaaguuggccccguaacuucgggagaaggggugcucccuggggugauga
gccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaaca
cagcucucugcgaacucguaagaggagguauagggagcgacgcuugcccg
gugccggaaggucaaggggaggggugcaagccccgaaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucgg
cgagggacccggugaaauugaacuggccgugaagaugcggccuacccgug
gcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcucu
uggucgcgccugcguaggauaggugggagccugugaacccccgccuccgg
gugggggggaggcgccggugaaauaccacccuggcgcggcugggggccua
acccucggauggggggacagcgcuuggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgg
aaauccgccggagagcgcaaggguagaagggggccugacugcgaggccug
caagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugu
ggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcug
aucucccccgagcguccacagcggcggggagguuuggcaccucgaugucg
gcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgc
ccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgg
ucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguac
gagaggaccggaagggacgcaccucugguuucccagcugucccuccaggg
gcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucua
agcgggaagcccgccccaagaugaggccucccacggcgucaagccgguaa
ggacccgggaagaccacccgguggaugggccggggguguaagcgccgcga
ggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5e Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): M11 R13 P22 R37 D42 Y44 P56 R58 N60 R61 P62 K64 H66 I77 L78 E80 R82 K109 G110 G112 F113 G115 K118 R119 F122 A123 P126 D127 S128 H129 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 V165 T166 M168 K185 A187 V188 P189 P191
• Binding residue (residue number reindexed from 1): M11 R13 P22 R37 D42 Y44 P56 R58 N60 R61 P62 K64 H66 I77 L78 E80 R82 K109 G110 G112 F113 G115 K118 R119 F122 A123 P126 D127 S128 H129 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 V165 T166 M168 K185 A187 V188 P189 P191

Gene Ontology

Molecular Function

• 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:4v5e, PDBe:4v5e, PDBj:4v5e
• PDBsum: 4v5e
• PubMed: 18988853
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)