Structure of PDB 4v4t Chain BF Binding Site BS01

Receptor Information

>4v4t Chain BF (length=189) Species: 274 (Thermus thermophilus)

MEATIYDNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAG
LRTPAESFGSGRGQAHRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVR
SALAATADVVVSDDFEDLVKTQEVVSLLEALDVHADIDRLFVTSDEPSTA
ARNLAGADVATASEVNTEDLAPGRLTVFTESALAEVAER

Ligand information

>4v4t Chain BA (length=2814)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcggcgcggcugggggccuaacccucggauggggggacagcgcuugg
cgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgccc
aaagguccccucaggcgggacggaaauccgccggagagcgcaaggguaga
agggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggc
cuagugaaccgguggucccguguggaagggccaucgaucaacggauaaaa
guuaccccggggauaacaggcugaucucccccgagcguccacagcggcgg
ggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaag
gucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguu
cagaacgucgugagacaguucggucucuauccgccacgggcgcaggaggc
uugaggggggcucuuccuaguacgagaggaccggaagggacgcaccucug
guuucccagcugucccuccaggggcauaagcuggguagccaugugcggaa
gggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggc
cucccacggcgucaagccgguaaggacccgggaagaccacccgguggaug
ggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgu
ccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4t Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.
• Resolution: 6.46 Å
• Binding residue (original residue number in PDB): R27 D29 L30 K33 Q39 R42 K43 Q44 Y46 S48 D49 A52 L54 R55 P57 E59 S60 G64 G66 Q67 H69 R79 V80 P81 Q82 A83 V84 K85 H90 K93 T94 D97 D101 N103 D104 K105 E106 Q108 L109 T150 D167 N206 L207 E217 N219 E221 D222 G230 L232
• Binding residue (residue number reindexed from 1): R24 D26 L27 K30 Q36 R39 K40 Q41 Y43 S45 D46 A49 L51 R52 P54 E56 S57 G61 G63 Q64 H66 R67 V68 P69 Q70 A71 V72 K73 H78 K81 T82 D85 D89 N91 D92 K93 E94 Q96 L97 T121 D138 N153 L154 E164 N166 E168 D169 G173 L175

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:4v4t, PDBe:4v4t, PDBj:4v4t
• PDBsum: 4v4t
• PubMed: 16377566
• UniProt: P12735|RL4_HALMA Large ribosomal subunit protein uL4 (Gene Name=rpl4)