Structure of PDB 6gzx Chain N2 Binding Site BS01

Receptor Information
>6gzx Chain N2 (length=111) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSA
SSLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKAL
AEGAREGGLEF
Ligand information
>6gzx Chain A2 (length=2912) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccga
aaaguccgcggccguggacccgaaaccgggcgagcuagcccuggccaggg
ugaagcuggggugagacccaguggaggcccgaaccggugggggaugcaaa
ccccucggaugagcuggggcuaggagugaaaagcuaaccgagcccggaga
uagcugguucuccccgaaaugacuuuagggucagccucaggcgcugacug
gggccuguagagcacugauagggcuagggggcccaccagccuaccaaacc
cugucaaacuccgaagggucccagguggagccugggagugagggcgcgag
cgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaagg
cccccaagucugggcuaagugguaaaggauguggcgccgcgaagacagcc
aggauguuggcuuagaagcagccaucauuuaaagagugcguaauagcuca
cuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgcc
gaagcugcgggucugggggaugaccccaggcgguaggggagcguucccga
ugccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcga
augccggcaugaguaacgauaaagagggugagaaucccucucgccguaag
cccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccua
aggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcc
cuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagcc
auggacgagcccggccagaagcgcagggugggagguaggcaaauccgccu
cccaacaagcucugcgugguggggaagcccguacgggugacaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucuugacc
......<.......<<<<<<<<<<<.........<<.<<<<.<<<<....
..<<<<<<.[...((.>>>.....<<<<<<<..<<<))...].>>>....
.>>>>>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<
<<<<.......>>>>>.>>....<<<<<...................>>>
>>...........<<....>>....<<<<.....<<.....>>....>>>
>....<<<....<<<<<<<<.....>>>>>>>>......<<..<<<<...
........<.......<...<<....<<<........>>>.((......<
<<.....))>>>...>>.....>........>......>>>>...>>...
..<<<<<<<<.........>>>>>>>>......<<<<.....<<.>>>>.
.>>>......>>..>>>>..>>...............<<....>>.....
..........<<<<....>>>>..................>>>>>>>>>>
>.......<<<<<<<<<<<....>>>>>>>>>>>................
..<<<<<<....<<<<<<<<<<<<...<<<...<<.......>>...>>>
...<<....>>..<<<<.....>>>>........................
....>>>>>>>>>>>>..<<.<...<<<<<<......<<<<<<<<...<<
....<<<<<<......>>>>>>.....>>.....<<...<<<........
>>.>.>>.....>>>>>>>>......<.....>........>>>>>>...
....>>>..<<<<<<....<<<<<....>>>>><.<<<<<<<.....<<<
<<<<<<...<<<...<<<<<<<<.<.....................>.>>
>>>>>>..>>.>...>>>>>>>>>.....>>>>>.>.>>..<<<<<<<.<
<......>>.>>>>>>>......<<......>>....<<<<.<<<...<<
<(((.....<<<<..<..........<<..<<<<<<<<<........<.<
.....................................<........>...
..>.>....>>>>>>>>>.>>..........)))......>.>>>>.>>>
...>>>>>>>...<.<<<.....>>>..>......>>>>>><..<<<<..
.<<<......<<<<<.<<<....>>>>>>>>...>>>..>>>.>..>...
..>>>>>>.......<<.....<<<<.<........>>>>>.<<<....<
<<<<.<.<...<<<<<.............>>>>>.....((.<<<.<<..
.<.<...<<<....>>>...>.>...>>....<<<<........>>>>.)
)<<<<<<<<<<<.....<<<<.....<<<..<<.<.<<<<<.<<<<.<<.
........>>>>>><<<....<<<<<<...<<<<.<..........>.>>
>>........>>>>>>...>>>....<<<<....>>>>......>>>>>.
..>>>...>>>..........>>>>........>>>>>>>>>>>>>>...
>>.....<<......>>>>>>>.<<<<<....>>>>>..>>>....<<<.
...<<<<<<<<..<.........<.....<<<<<....<....>.....>
>>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<
<<....<<.<........>>>..<<<<<<<......<.......>.....
..>>>>>>>...<<<.<<<..<<<<<<<..<<<...<<...<<<<<....
>>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>...
.....<...........<<<<<<.....>>>>>>.....>....>>>...
....>>>>>>>..>..>..>>>>>>>>.>>>.>>...........<<<<.
.........>>>>..<<<<<<<<.<<<..........<<<.<<.<<...<
<<<<.<<<.<.<<<.<<<<<<.............................
..................................................
.............>>>>>>...<<<<......>>>>....>>>.>.>>>.
.>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<..
..<<<<<<...<<<<.<.......>.>>>>.....<.....((.>....>
>>>>>....<<....................>>.<<......>>.>>)).
........<<<<<<.<<..>>....>>>>>>>>...............>>
...>>>>.>.......<<<<.<.<<<<<<...<<.......>>...>>>>
>>...>>>>.>.......<.<<<.<<<<<...<<<<<<<..........>
>>>..>>>.<<<<<.....>>>>>......>>>>..>...>>>..>....
<<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<.<..
..<<<<..<<<<<<<...............>>>>>>>.<<<<<....<.<
...<<<<<.<<<<......>>>>....>>>>>...>.>..>>>>>...<<
<....<<<<<...........>>>>.>...>>>.>>>>........>.>>
>>..<<.........>>....<<<<<<<<<.......>>>>>....<<<.
<<<<.<<<....<<<<<....>>>>>...>>>..>>>>..>>>...>>>>
.....>......
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]
PDB6gzx Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
Resolution4.57 Å
Binding residue
(original residue number in PDB)		R3 R9 R10 F12 R13 N16 R17 T21 R89 K93 Y94 E111 F112
Binding residue
(residue number reindexed from 1)		R2 R8 R9 F11 R12 N15 R16 T20 R88 K92 Y93 E110 F111
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
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:6gzx, PDBe:6gzx, PDBj:6gzx
PDBsum6gzx
PubMed30301898
UniProtQ5SHQ4|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)

[Back to BioLiP]