Structure of PDB 5mmm Chain C Binding Site BS01

Receptor Information

>5mmm Chain C (length=253) Species: 3562 (Spinacia oleracea)

QVKSNPRNNLISGQRRCGKGRNARGIITARHRGGGHKRLYRKIDFRRNEK
DIYGKIVTIEYDPNRNAYICLIHYGDGEKRYILHPRGAIIGDTIVSGTEV
PIKMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAKLIAKEGKSA
TLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAGSKRWLGKRPVVRG
VVMNPVDHPHGGGEGRAPIGRKSPTTPWGYPALGRRSRKRNKYSDNFIIR
RRS

Ligand information

>5mmm Chain A (length=2798)

ucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagga
agggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagaga
uccggagauucccgaauaggucaaccuuucgaacuucugcugaauccaug
ggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagga
aaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagcag
ccuaaaccgugaaaacgggguugugggagagcaauacaagcgucgugcug
cuaggcgaaucaguggagugcggaacccuagauggugaaaguccaguagc
cgaaagcaucacuagcuuaugcucugacccgaguagcauggggcacgugg
aaucccgugugaaucagcaaggaccaccuugcaaggcuaaauacuccugg
gugaccgauagcgaaguaguaccgugagggaagggugaaaagaaccccca
ucggggagugaaaagaacaugaaaccguaagcucucaagcagugggaggg
ggaccagacccugaccgcgugccuguugaagaaugagccggcgacucaua
ggcaguggcuugguuaagggaacccaccggagccguagcgaaagcgaguc
uucauagggcaauugucacugcuuauggacccgaaccugggugaucuauc
caugaccaggaugaagcuugggugaaacuaaguggagguccgaaccgacu
gauguugaagaaucagcggaugaguugugguuaggggugaaaugccacuc
gaacccagagcuagcugguucuccccgaaaugcguugaggcgcagcaguu
gacuggacaucuagggguaaagcacuguuucggugcgggccgccgguacc
aaaucgaggcaaacucugaauacuagauaugaccuccaaauaacaggggu
caaggucggccagugagacgaugggggauaagcuucaucgucgagaggga
aacagcccggaucaccagcuaaggccccuaaaugaccgcucagugauaaa
ggagguaggggugcagagacagccaggagguuugccuagaagcagccacc
cuugaaagagugcguaauagcucacugaucgagcgcucuugcgccgaaga
ugaacggggcuaagcggucugccgaagcugugggauguaaaaaaacaucg
guaggggagcguuccguguuagggagaaacgcgugcgugagccgcguugg
acgaagcggaagcgagaaugucggcuugaguaacgcaaacauuggugaga
auccaaugccccgaaaaccuaaggguuccuccgcaagguucguccacgga
gggugagucagggccuaagaucaggccgaaaggcguagucgauggacaac
aggugaauauuccuguacuaccccuuguuggucccgagggacggaggagg
cuagguuagccgaaagaugguuaucgguucaaggacgcaaggugacccug
uuuuucaggguaagaagggguagagaaaaugccucgagccaauguucgag
uaccaggcgcuacggcgcugaaguaaccgaugccauacucccaggaaaag
cucgaacgaccuucaacaaaaggguaccuguacccgaaaccgacacaggu
agguagguagagaauaccuaggggcgcgagacaacucucucuaaggaacu
cggcaaaauagccccguaacuucgggagaaggggugcccccucggggguc
gaagugaccaggcccgggcgacuguuuaccaaaaacacaggucuccgcaa
agucguaagaccauguaugggggcugacgccugcccagugccggaagguc
aaggaaguuggugaccugaugacaggggagccggcgaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgacccgcacgaaaggcguaacgaucugggcacugucucgg
agagaggcucggugaaauagacaugucugugaagaugcggacuaccugca
ccuggacagaaagacccuaugaagcuuuacuguucccugggauuggcuuu
gggcuuuuccugcgcagcuuagguggaaggcgaagaaggcccccuuccgg
gggggcccgagccaucagugagauaccacucuggaagagcuagaauucua
accuugugucaggaccuacgggccaagggacauucucagguagacaguuu
cuauggggcguaggccucccaaaagguaacggaggcgugcaaagguuucc
ucgggccggacggagauuggcccucgagugcaaaggcagaagggagcuug
acugcaagacccacccgucgagcagggacgaaagucggccuuagugaucc
gacggugccgaguggaagggccgucgcucaacggauaaaaguuacucuag
ggauaacaggcugaucuuccccaagaguucacaucgacgggaagguuugg
caccucgaugucggcucuucgccaccuggggcuguaguauguuccaaggg
uugggcuguucgcccauuaaagcgguacgugagcuggguucagaacgucg
ugagacaguucgguccauauccggugugggcguuagagcauugagaggac
cuuucccuaguacgagaggaccgggaaggacgcaccucugguguaccagu
uaucgugcccacgguaaacgcuggguagccaagugcggagcggauaacug
cugaaagcaucuaaguaguaagcccaccccaagaugagugcucuccua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mmm The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): V20 R25 N27 G31 K37 G38 R39 N40 A41 R42 I45 T46 A47 R48 R50 G52 K55 R56 L57 Y58 R59 R64 Y79 R83 N84 D94 G95 K97 R146 Q149 L150 A151 R152 A153 A154 K166 L172 P173 S174 E176 R178 V194 N197 R200 L201 G202 R203 A204 G205 K207 R208 W209 R213 P214 V215 V216 R217 G218 V219 V220 M221 N222 V224 D225 H226 H228 G230 G231 E232 G233 R234 P236 I237 G238 R239 P242 P245 W246 Y248 L251 G252 R254 S255 R256 K257 K260 Y261 S262 R269 R270
• Binding residue (residue number reindexed from 1): V2 R7 N9 G13 K19 G20 R21 N22 A23 R24 I27 T28 A29 R30 R32 G34 K37 R38 L39 Y40 R41 R46 Y61 R65 N66 D76 G77 K79 R128 Q131 L132 A133 R134 A135 A136 K148 L154 P155 S156 E158 R160 V176 N179 R182 L183 G184 R185 A186 G187 K189 R190 W191 R195 P196 V197 V198 R199 G200 V201 V202 M203 N204 V206 D207 H208 H210 G212 G213 E214 G215 R216 P218 I219 G220 R221 P224 P227 W228 Y230 L233 G234 R236 S237 R238 K239 K242 Y243 S244 R251 R252

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:0009507 chloroplast
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mmm, PDBe:5mmm, PDBj:5mmm
• PDBsum: 5mmm
• PubMed: 28007896
• UniProt: P06509|RK2_SPIOL Large ribosomal subunit protein uL2cz/uL2cy (Gene Name=rpl2-A)