Structure of PDB 6xyw Chain Ab Binding Site BS01

Receptor Information

>6xyw Chain Ab (length=155) Species: 3702 (Arabidopsis thaliana)

NSMIGSSMPLGMMRIGTIIHNIEMNPGQGAKMVRAAGTNAKILKEPAKGK
CLIKLPSGDTKWINAKCRATIGTVSNPSHGTKKLYKAGQSRWLGIRPKVR
GVAMNPCDHPHGGGEGKSKSSGSRGRTSVSPWGKPCKGGYKSASVKKKKK
RLAEA

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

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): K86 M87 V88 R89 A90 A91 G92 L110 S112 D114 K116 H134 G135 K138 L139 Y140 K141 A142 G143 R146 W147 R151 P152 K153 V154 R155 G156 V157 A158 M159 N160 C162 D163 G169 E170 G171 K172 S175 S176 G177 S178 R179 G180 R181 T182 S183 W187 C191 K192 G193 G194 Y195 K196 A198 K201 K202 K203
• Binding residue (residue number reindexed from 1): K31 M32 V33 R34 A35 A36 G37 L55 S57 D59 K61 H79 G80 K83 L84 Y85 K86 A87 G88 R91 W92 R96 P97 K98 V99 R100 G101 V102 A103 M104 N105 C107 D108 G114 E115 G116 K117 S120 S121 G122 S123 R124 G125 R126 T127 S128 W132 C136 K137 G138 G139 Y140 K141 A143 K146 K147 K148

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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: Q8VZU4|RM02C_ARATH Large ribosomal subunit protein uL2my, C-terminal part (Gene Name=RPL2-C)