Structure of PDB 8rdv Chain VH Binding Site BS01

Receptor Information
>8rdv Chain VH (length=84) Species: 45610 (Psychrobacter urativorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AHKKAAGSSRNGRDSNPKMLGVKIFGGQAIVAGNIIVRQRGTEFHAGAGV
GMGRDHTLFALNDGVVKFATKGKFNRRYVMVEEA
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
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<<..>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>...
......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<<
<..<<<<<<<<<<<<<.<<<...<<<<........>>>>((......<<<
.....))>>>...>>>...>>>>>>>>>>>>>...........<<<<<<<
<.........>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>>.>>>..............<<....>>....>>.......
..<<<<.....>>>>..................>>>>>>>>>>>......
.<<<<..<<<<<<<....>>>>>>>..>>>>...<............>.<
<<<<<....<<<<<<<<<<<<<..<<<...<<.....>>...>>>...<<
....>>..<<<<.....>>>>.....>>>>>>>>>>>>>..<<.<...<<
<<<<.....<<<<<<<<<..<<<<....<<<<<......>>>>>..>...
>>>...<<<.<<<.<........>.>>>>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>>.<<<<<<<....<<<<<<<<<.....<<<...<<<.<<<<..>>
>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>.>...<<<<<<<<<
<......>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<
(((.....<<<<<<...........<<..<<<<<..<<........<<<<
<.<<<..<<<<.......>>>>..>>>........<<<......>>>..>
>>>>....>>..>>>>>.>>...........)))......>>>>>>.>>>
...>>>>>>><<<<<<.<.....>.>>>>>>....>>>>>>..<<<<<..
.<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.......
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...
<<<...<<<....>>>...>>>...>>>..<<<<<........>>>>>))
<<<<<<<<<<<.<...<<<<....<<<<..<<<..<<<<<<<<<<<...[
[[[...>>>>>>....<<<<...<<<<<<<<<<<..<<.....>>.>>>>
>>>>>>>...>>>>.............>>>>>...>>>...>>>>.....
....>>>>...>>>>>>>>>>>>.>>>..>>.....<<......>>>>>>
>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<........
.......<<<<<...............>>>>><<<<<<<<.<<<...<<<
...>>>...>>>.>>>>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<....<...<<<<<<.<<....>>..>>>>
>>..>.....>>>>>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<<.....>>>>>>.....>....>>>>>..>>
.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<...
.....>>>>>..<<<<<<<.<<<<.<<......<<<<.<<<<<<..<<<<
<.<<<.<<<<<.<<<<<..>>>>>...<<<.<<<<<....>>>>>>>>..
..>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.<<..))))..>>>>>>>>>....
.........>>>>..>>>>>>.......<<<<...<<<<<<...<<....
...>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<<
<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>.
..>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>
....<<<<<<<...<<<<..<<<<<<.................>>>>>>.
<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>..>>>>>...>>>>
.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>>.
......>>>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<
<..<<....<<<<<....>>>>>...>>...>>>>>.>>>...>>>>...
..>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8rdv A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis
Resolution2.6 Å
Binding residue
(original residue number in PDB)
R11 N12 R14 D15 S16 N17 P18 K19 M20 L21 K24 F26 G27 Q29 A33 G34 N35 I36 R39 R41 G42 T43 E44 H46 G54 R55 D56 H57 F60 F69 F75 R77 R78
Binding residue
(residue number reindexed from 1)
R10 N11 R13 D14 S15 N16 P17 K18 M19 L20 K23 F25 G26 Q28 A32 G33 N34 I35 R38 R40 G41 T42 E43 H45 G53 R54 D55 H56 F59 F68 F74 R76 R77
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
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
UniProtA0A0M4TUE5

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