Structure of PDB 4v85 Chain B2 Binding Site BS01

Receptor Information

>4v85 Chain B2 (length=63) Species: 562 (Escherichia coli)

MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDV
ARVKTLLNEKAGA

Ligand information

>4v85 Chain BA (length=2853)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaaggggguccuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgaugugggaaggcccagacagccagga
uguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugg
ucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaag
cugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagc
cugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugc
ugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacca
aggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggc
gaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuug
guguuacugcgaaggggggacggagaaggcuauguuggccgggcgacggu
ugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauc
aaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcc
cugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccc
aaaccgacacagguggucagguagagaauaccaaggcgcuugagagaacu
cgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacg
cugauauguaggugaggucccucgcggauggagcugaaaucagucgaaga
uaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacg
aaaguggacguauacggugugacgccugcccggugccggaagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auggaaguguggacgccagucugcauggcuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v85 Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): K2 Q38 Q39 S40 H41 R47 R48 A51 R52 K54 T55 N58
• Binding residue (residue number reindexed from 1): K2 Q38 Q39 S40 H41 R47 R48 A51 R52 K54 T55 N58

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v85, PDBe:4v85, PDBj:4v85
• PDBsum: 4v85
• PubMed: 22187675
• UniProt: P0A7M6|RL29_ECOLI Large ribosomal subunit protein uL29 (Gene Name=rpmC)