Structure of PDB 8rdv Chain TI Binding Site BS01

Receptor Information
>8rdv Chain TI (length=102) Species: 45610 (Psychrobacter urativorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKLRKGDTVIVIAGKDKGKQGTVQAVKNDRIKVEGINIVTKHQKPNQATG
VEGGILKQEAFLHISNVAILNAQTQKADRITYQFGEDGKKQRVYRSNGEV
VA
Ligand information
>8rdv Chain Z2 (length=2710) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gucaaguaaugaagcgcacaugguggaugccuuggcagucagaggcgaug
aaagacgugacagccugcgauaagcuucggggaggcggcaauauccugug
auccggagauuucugaauggggaaacccacuuaccauaagguagguaucu
uguacaagaagcgaacgaggggaagugaaacaucucaguacccuuaggaa
aagacaucaaaugagauuccccaaguagcggcgagcgaacggggagaagc
cgauuaaugcuaauguagaagaacagcgugggaaagcugaccguaguagg
ugauaguccuguauucgaaacauuagcguuaacauauuaaguagggcggg
acacgagaaauccugucugaagauggggggaccauccuccaaggcuaaau
acuccugacugaccgauagugaaccaguaccgugagggaaaggcgaaaag
aaccccugugaggggagugaaauagaaccugaaaccgugugcguacaagc
aguaggagccucaauuuauuggggugacugcguaccuuuuguauaauggg
ucagcgacuuauauucuguagcaagguuaaccguuuaggggagccguagg
gaaaccgagucuuaauagggcgucuaguugcaggguauagacccgaaacc
gagugaucuauccaugagcagguugaaagugccguaacaggcaccggagg
accgaacccacugucguugaaaagccaggggaugacuuguggauaggggu
gaaaggcuaaucaaacucggugacagcugguucuccccgaaagcuauuua
gguagcgccucggacgaauaccauuggggguagagcacuguuucggcacc
gaugcaaacuccgaauaccgaugaguaauauccgggagacacacggcggg
ugcuaacguccgucguggagagggaaacaacccagaccgccagcuaaggc
cccaaauuccuaguuaagugggaaacgaggugggaaggcauagacagcua
ggagguuggcuuagaagcagccauccuuuaaagaaagcguaauagcucac
uagucgagucggccugcgcggaagauguaacggggcucaaacuaggagcc
gaagcugcggauuugaaacuuguuuucaagugguaggggagcguugugua
agccugugaaggugugucguaaggcaugcuggagguaucacaagagcgaa
ugcugacgugaguaacgauaaugcgagugaaaagcucgcacgccggaaga
ucaaggguuccaguccaacguuaaucggggcugggugagucgaccccuaa
ggcgaggccgaaaggcguagucgaugggaaauugguuaauauuccaauac
uuguuuauagugcgauggagggacggagaagguuaugucagccuggcguu
gguuguccaggugaaaggauguaggcuuacaguuuaggcaaauccggacu
guaggcugagaucugauagcaaggaaguggcaaauaccaugcuuccagga
aaagcuucuaaggcuauaaacgaaucguacccuaaaccgacacaggugau
cagguagagaauaccaaggcgcuugagagaacucugcugaaggaacuagg
caaaaugguaccguaacuucgggagaagguacgcuguugauggugauagg
ucuccuugagcuuucgacagucgcagauaccaggcugcugcaacuguuua
uuaaaaacacagcacucugcaaacacgaaaguggacguauagggugugau
gccugcccggugcuggaagguuaauugaugggguuagcguaagcgaagcu
cuugaucgaagccccaguaaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucagguaaguucugaccugcacgaauggcauaaug
auggcagcgcugucuccagcagagacucagugaaaucgaaaucgcaguga
agaugcuguguacccgcggcuagacggaaagaccccgugaaccuuuacua
cagcuuuacauugaacuuggguucuaacucagguauaacaauaccgagga
caauguaugguggguaguuugacuggggcggucuccuccuaaagaguaac
ggaggaguacgaaggugcgcucagaacggucggaaaucguucauagagua
uaaaggcaaaagcgcgcuuaacugcgagacccacaagucgagcagguacg
aaaguaggucuuagugauccggugguucuguauggaagggccaucgcuca
acggauaaaagguacucuggggauaacaggcugauaccgcccaagaguuc
auaucgacggcgguguuuggcaccucgaugucggcucaucucauccuagg
gcugaagcagguccuaaggguauggcuguucgccauuuaaagagguacgc
gagcuggguuuagaacgucgugagacaguucggucccuaucuaccguggg
cguuggaaauuugagaggaucugcuccuaguacgagaggaccagagugga
cgaaccucugguguucggguugucacgccaguggcauugcccgguagcua
cguucggaugggauaaccgcugaaagcaucuaagcgggaagcccaccuca
agauuagauuucccuaaagagccguugaagacuacgacguugauaggcag
gguguggaagugcagcgaugcauguagcuaaccuguacuaauugcucguu
uggcuugacc
<<<<<<<......<<<<<<<<<<<.....<<.<<<<<<<<<<<<<<....
..<<<<<<.[..(((.>>>.....<<<<<<<..<<.)))..]..>>....
.>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<<
<<..>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>...
......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<<
<..<<<<<<<<<<<<<.<<<...<<<<........>>>>((......<<<
.....))>>>...>>>...>>>>>>>>>>>>>...........<<<<<<<
<.........>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>>.>>>..............<<....>>....>>.......
..<<<<.....>>>>..................>>>>>>>>>>>......
.<<<<..<<<<<<<....>>>>>>>..>>>>...<............>.<
<<<<<....<<<<<<<<<<<<<..<<<...<<.....>>...>>>...<<
....>>..<<<<.....>>>>.....>>>>>>>>>>>>>..<<.<...<<
<<<<.....<<<<<<<<<..<<<<....<<<<<......>>>>>..>...
>>>...<<<.<<<.<........>.>>>>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>>.<<<<<<<....<<<<<<<<<.....<<<...<<<.<<<<..>>
>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>.>...<<<<<<<<<
<......>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<
(((.....<<<<<<...........<<..<<<<<..<<........<<<<
<.<<<..<<<<.......>>>>..>>>........<<<......>>>..>
>>>>....>>..>>>>>.>>...........)))......>>>>>>.>>>
...>>>>>>><<<<<<.<.....>.>>>>>>....>>>>>>..<<<<<..
.<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.......
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...
<<<...<<<....>>>...>>>...>>>..<<<<<........>>>>>))
<<<<<<<<<<<.<...<<<<....<<<<..<<<..<<<<<<<<<<<...[
[[[...>>>>>>....<<<<...<<<<<<<<<<<..<<.....>>.>>>>
>>>>>>>...>>>>.............>>>>>...>>>...>>>>.....
....>>>>...>>>>>>>>>>>>.>>>..>>.....<<......>>>>>>
>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<........
.......<<<<<...............>>>>><<<<<<<<.<<<...<<<
...>>>...>>>.>>>>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<....<...<<<<<<.<<....>>..>>>>
>>..>.....>>>>>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<<.....>>>>>>.....>....>>>>>..>>
.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<...
.....>>>>>..<<<<<<<.<<<<.<<......<<<<.<<<<<<..<<<<
<.<<<.<<<<<.<<<<<..>>>>>...<<<.<<<<<....>>>>>>>>..
..>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.<<..))))..>>>>>>>>>....
.........>>>>..>>>>>>.......<<<<...<<<<<<...<<....
...>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<<
<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>.
..>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>
....<<<<<<<...<<<<..<<<<<<.................>>>>>>.
<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>..>>>>>...>>>>
.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>>.
......>>>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<
<..<<....<<<<<....>>>>>...>>...>>>>>.>>>...>>>>...
..>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8rdv A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis
Resolution2.6 Å
Binding residue
(original residue number in PDB)
R5 K6 G15 K16 V40 T41 K42 H43 Q44 K45 P46 G55 I56 H64 S66 N67 R80 T82 Y83 K91 R96
Binding residue
(residue number reindexed from 1)
R4 K5 G14 K15 V39 T40 K41 H42 Q43 K44 P45 G54 I55 H63 S65 N66 R79 T81 Y82 K90 R95
Enzymatic activity
Enzyme Commision number ?
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:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8rdv, PDBe:8rdv, PDBj:8rdv
PDBsum8rdv
PubMed38355796
UniProtA0A0M4TE60

[Back to BioLiP]