Structure of PDB 6gzx Chain C1 Binding Site BS01

Receptor Information
>6gzx Chain C1 (length=272) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIAR
Ligand information
>6gzx Chain A1 (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
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<<<<.......>>>>>.>.....<<<<<...................>>>
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....<.........<<<<.<<.....<<<........>>>.((......<
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<......>>.>>>>>>>......<<......>>....<<<<.<<<...<<
<((.(....<<<<.............<<..<<<<.<<<.........<<<
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.<<<......<<<<<.<<<....>>>>>>>>...>>>...>.....>...
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).<<<<<<<<.......<<<<.....<<<.....<.<<<<<.<<<<.<<.
........>>>>>>.......<<<<<<..<<<<<<<..........>>>>
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>>.....<<......>>.>>>>.<<<<......>>>>..>>>>...<<<.
...<<<<<<<<..<...............<<<<<....<<..>>.....>
>>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<
<<<<..<<<.........>>>..<<<<<<<....................
..>>>>>>>...<<<.<<<..<<<<<<<..<<<...<....<<<<<....
>>>>>....>...>>>>>>>>..>>>>><<<<<<.......>>>>>>...
.....<...........<<<<<<.....>>>>>>.....>....>>>...
.>>.>>>>>>>.....>..>>>>>>>>.>>>.>>...........<<<<<
........>>>>>..<<<<<<<<.<<<..........<<<.<<.<<<..<
<<<<.<<<.<<<<<.<<<<<<.............................
.........<<..............>>.......................
.............>>>>>>...<<<<......>>>>....>>>>>.>>>.
.>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<..
..<<<<<<...<<<<.<.......>.>>>>.....<.....((.>....>
>>>>>....<<<..................>>>.<<......>>.>>)).
........<<<<<<.<<..))))..>>>>>>>>..............>>>
...>>>>>........<<<<.<.<<<<<<...<<.......>>...>>>>
>>...>>>>.>.........<<<..<<<<...<<<<<<<<........>>
>>>..>>>.<<<<<.....>>>>>......>>>>......>>>.......
<<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<<<.
..<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<
...<<<<<.<<<<......>>>>....>>>>>...>>>>.>>>>>...<<
<....<.<<<...........>>>..>...>>>.>>>>.......>>>>>
>>..<<<.......>>>....<<<<<<<<<.......>>>>>....<<<.
<<<<.<<<.....<<<<....>>>>....>>>..>>>>..>>>...>>>>
.....>>.>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)
K4 P8 Y9 P11 S12 R14 V18 F21 E28 L33 K39 R43 N45 G47 R48 I49 T50 R52 R54 R60 R63 Y84 P86 R88 H96 Y97 V98 D99 G100 E101 K151 K154 L155 A156 R157 A158 G160 T161 H186 H201 K202 V205 L206 G207 K208 A209 R213 W214 R217 R218 V221 R222 G223 A225 M226 N227 V229 H231 H233 G235 E237 G238 R239 A240 P241 R242 G243 R244 P249 W250 W252 T254 K255 L257 K258 T259 R260 K261 R262 P265 S266 R268
Binding residue
(residue number reindexed from 1)
K3 P7 Y8 P10 S11 R13 V17 F20 E27 L32 K38 R42 N44 G46 R47 I48 T49 R51 R53 R59 R62 Y83 P85 R87 H95 Y96 V97 D98 G99 E100 K150 K153 L154 A155 R156 A157 G159 T160 H185 H200 K201 V204 L205 G206 K207 A208 R212 W213 R216 R217 V220 R221 G222 A224 M225 N226 V228 H230 H232 G234 E236 G237 R238 A239 P240 R241 G242 R243 P248 W249 W251 T253 K254 L256 K257 T258 R259 K260 R261 P264 S265 R267
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0016740 transferase activity
GO:0019843 rRNA binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6gzx, PDBe:6gzx, PDBj:6gzx
PDBsum6gzx
PubMed30301898
UniProtP60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)

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