Structure of PDB 6xyw Chain Ac Binding Site BS01

Receptor Information

>6xyw Chain Ac (length=218) Species: 3702 (Arabidopsis thaliana)

EAKQGEMSSRSKRTGIIAVKCGMTALWDKWGKRIPISILWVDDNIVSQVK
TVEKEGIFALQIGCGQKKPKHLSKAVVGHFRAQGVPLKRKLREFPVTEDA
LLPVGTSLGVRHFVPGQYVDVTGITRGKGFQGCMKRHGFSGMPASHGASL
SHRSGGSTGQRDAPGKVFKGRKMAGRMGADQRTVKNVWVYKIDPARNLMW
VRGQVPGAEGNFVFIKDA

Ligand information

>6xyw Chain 1 (length=2842)

gaaugcauuggauggaugcccgggcauugagaaggaaggacgcuuucaga
ggcgaaaggccauggggagauaccgucugugauccauggaucuccgaucg
ggaaaccguauccaagcuccguggcuagucugcgcucuuuggacuuugaa
aacuuagcgaacugaaacaucuaaguagcuaaaggaagggaaaucaaccg
agaccccguuaguagcggcgagcgagagcggauuugggauuuuaagaaaa
agaaagacgaagcacuucuuuuucgccagguuuacuguaauugugaaaag
guuggaagaucuggccaaagaaggugauagccccguagauucguuccuau
gguucgauccuucccaguaaaacgcggcguguucgaauucugaucgcuuu
uacgcgagaaagggggaccacccucuaagccuaaguauuccucaaugacc
gauagcguacaaguaccgugagggaaaggugaaaagaacccuaugacggg
agugcaauagagaaccugagauccgaugcgaacaaucagucgaaggagua
gucaagcgcacucacucuaacggcguaccuuuugcaugaugggucagcga
ggaaaugggaagagcggcuuaagccauuagguguaggcgcuuuccaaagg
uggaaucuucuaguucuuccuauuugacccgaaaccgaucgaucuagcca
ugagcagguugaagagagcucuaacaggccuuggaggaccgaacccacgu
auguggcaaaauacggggaugacuuguggcuaggggugaaaggccaacca
agaucggauauagcugguuuuccgcgaaaucuauuucaguagagcguaug
augucgauggcccgagguagagcacucaaugggcuaggguggcuuaccaa
ccccagggaaacuccgaauacaggccguucucguuuguacagacagacuu
uuggggugcuaagauccaaagucgagagggaaacagcccagaucguacgc
uaaggucccuaagcaaucacuuaguggaaaaggaagugaucgagcgauga
caaccaggaggugggcuuggaagcagccauccuuugaagaaagcguaaua
gcucacuggucuagcuccauggcaccgaaaauguaucagggcucaaguga
uucaccgaagcgacgagaccuugaaagcugcuuuuucaagugucaguagc
ggaacguucugucaaucggggaagguuuuuggugacaagaccuggagaua
ucagaagugagaaugcugacaugaguaacgauaaauccugugaaaaacac
gaucgccugccaguggaaggcuuucugcguucagucaaucuacgcagagu
gaaucggucccuaaggaacccccgaaagggcugccguccgauggguacac
gaaagugacgaaguugcuuugacuacaaaaccaugccucucucuuggagc
gaauuggaugaucgggccgagggcagcguagcgccucuuccccucacucu
ccuuucuccaauaugaaccuugagucaucaaaggcgagucuguuuauagu
cgcgacucuugucauagucaagaagguugaaacuuccaggaaaaaacuuc
gaauugggagggcgauccucccggugaacugaccguaccccaaaccgaca
caggugaacaaguagaguauacuagggcgcuugagagaaccaugucgaag
gaacucggcaaaaugaccccguaacuucgggagaaggggugcucuccuau
cuuuugauuaggaaagcggcacauaccaggggguagcgacuguuuauuaa
aaacacaggacucugcuaagugguaacacgauguauagagucugacaccu
gcccggugcuggaaagucaaaaggagaaguguuauaagcuuugaauggaa
gccccgguaaacggcggcaguaacucuaacuguccuaagguagcgaaauu
ccuugucgcauaaguagcgaccugcacgaaugguguaacgacugccccgc
ugucuccgacauggacccggugaaauugaauucuccgugaagaugcggag
uaccaacggcuagacgguaagaccccgugcaccuucacuauagcuucgca
gugacaaccuugaucgaauguguaggauaggugggaggucgugacauaga
aggaccaauccugaaagaccacucuuucgucuaagggugccuaaccgccg
cggcgggacacugcgagguggguaguuuaucuggggcggaugccuccuaa
agaguaacggaggugugcgaagguaggcucaagcuaagauucugcucgug
agcguaaugguauaagccugccugacugugagaccgacuggucgaacaga
gacgaaagucggccauagugauccgggagucccguguggaagggcucucg
cucaacggaucaaagguacgccggggauaacaggcugaugacucccaaga
gcucuuaucgacggagucguuuggcaccucgaugucgacucaucacaucc
ugggguugaagaaggucccaaggguucgguuguucgccgauucaaguggu
acgugaguuggguuuagaacgucgugagacaguucgguuccuaucuaccg
uugguguuaaagggagaacugcgaggagccaacccuaguacgagaggacu
ggguugggccaaccuaugguguaccgguuguuaugccaauagcagcgccg
ggcagcuaaguugguauggaagaacugcugcuuagcgggaaauccuucuc
uauacaaguucucggaacagguuuuagaacagaacuucgauaggcgggag
guggaagcaccgcgaggugugaagccaucucguacuaaacga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xyw Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.
• Resolution: 3.86 Å
• Binding residue (original residue number in PDB): K83 M86 R96 K113 E118 Q124 K131 K133 H134 K137 A138 G141 H142 R155 E156 T188 R189 G190 K191 G192 F193 Q194 G195 F202 M205 S208 A211 L213 H215 R216 G218 G219 T221 G222 Q223 R224 D225 P227 G228 K229 V230 F231 K232 K235 M236 A237 G238 R239 D243 R245 V250 G266 Q267 A271 E272 N274 F275
• Binding residue (residue number reindexed from 1): K20 M23 R33 K50 E55 Q61 K68 K70 H71 K74 A75 G78 H79 R92 E93 T125 R126 G127 K128 G129 F130 Q131 G132 F139 M142 S145 A148 L150 H152 R153 G155 G156 T158 G159 Q160 R161 D162 P164 G165 K166 V167 F168 K169 K172 M173 A174 G175 R176 D180 R182 V187 G203 Q204 A208 E209 N211 F212

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xyw, PDBe:6xyw, PDBj:6xyw
• PDBsum: 6xyw
• PubMed: 32251374
• UniProt: Q9LRN8|RK3B_ARATH Large ribosomal subunit protein uL3m (Gene Name=RPL3B)