Structure of PDB 5mlc Chain H Binding Site BS01

Receptor Information

>5mlc Chain H (length=178) Species: 3562 (Spinacia oleracea)

ESRIGKQPITVPANVAIAMEGQDLKVKGPLGELSITYPREVLVEKQESGF
LRVRKAVETRRANQMHGLFRTLTDNMVVGVSKGFEKKLQLVGVGYRATVE
GKDLILSLGFSHPVRMAIPDELQVKVEENTKVTVSGRDKSVVGQFAATIR
SWRPPEPYKGKGVRYVDEVVRRKEGKAG

Ligand information

>5mlc Chain A (length=2750)

uucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagg
aagggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagag
auccggagauucccgaauaggucaaccuuucgaacuucugcugaauccau
gggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagg
aaaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagca
gccuaaaccgugaaaacgggguugugggagaggcugcuaggcgaaucagu
ggagugcggaacccuagauggugaaaguccaguagccgaaagcaucacuc
ugacccgaguagcauggggcacguggaaucccgugugaaucagcaaggac
caccuugcaaggcuaaauacuccugggugaccgauagcgaaguaguaccg
ugagggaagggugaaaagaacccccaucggggagugaaauagaacaugaa
accguaagcucucaagcagugggagggggaccagacccugaccgcgugcc
uguugaagaaugagccggcgacucauaggcaguggcuugguuaagggaac
ccaccggagccguagcgaaagcgagucuucauagggcaauugucacugcu
uauggacccgaaccugggugaucuauccaugaccaggaugaagcuugggu
gaaacuaaguggagguccgaaccgacugauguugaagaaucagcggauga
guugugguuaggggugaaaugccacucgaacccagagcuagcugguucuc
cccgaaaugcguugaggcgcagcaguugacuggacaucuagggguaaagc
acuguuucggugcgggccgcgagagcgguaccaaaucgaggcaaacucug
aauacuagauaugaccuaggggucaaggucggccagugagacgauggggg
auaagcuucaucgucgagagggaaacagcccggaucaccagcuaaggccc
cuaaaugaccgcucagugauaaaggagguaggggugcagagacagccagg
agguuugccuagaagcagccacccuugaaagagugcguaauagcucacug
aucgagcgcucuugcgccgaagaugaacggggcuaagcggucugccgaag
cugugggauguaaaaaaacaucgguaggggagcguuccguguuagggaga
aacgcgugcgugagccgcguuggacgaagcggaagcgagaaugucggcuu
gaguaacgcaaacauuggugagaauccaaugccccgaaaaccuaaggguu
ccuccgcaagguucguccacggagggugagucagggccuaagaucaggcc
gaaaggcguagucgauggacaacaggugaauauuccuguacuaccccuug
uuggucccgagggacggaggaggcuagguuagccgaaagaugguuaucgg
uucaaggacgcaaggugaagggguagagaaaaugccucgagccaauguuc
gaguaccaggcgcuacggcgcugaaguaaccgaugccauacucccaggaa
aagcucgaacgaccuucaacaaaaggguaccuguacccgaaaccgacaca
gguagguagguagagaauaccuaggggcgcgagacaacucucucuaagga
acucggcaaaauagccccguaacuucgggagaaggggugcccccucacaa
agggggucgaagugaccaggcccgggcgacuguuuaccaaaaacacaggu
cuccgcaaagucguaagaccauguaugggggcugacgccugcccagugcc
ggaaggucaaggaaguuggugaccugaugacaggggagccggcgaccgaa
gccccggugaacggcggccguacgguccuaagguagcgaaauuccuuguc
ggguaaguuccgacccgcacgaaaggcguaacgaucugggcacugucucg
gagagaggcucggugaaauagacaugucugugaagaugcggacuaccugc
accuggacagaaagacccuaugaagcuuuacuguucccugggauuggcuu
ugggcuuuuccugcgcagcuuagguggaaggcgaagaaggcccccuuccg
ggggggcccgagccaucagugagauaccacucuggaagagcuagaauucu
aaccuugugucaggaccuacgggccaagggacauucucagguagacaguu
ucuauggggcguaggccucccaaaagguaacggaggcgugcaaagguuuc
cucgggccggacggagauuggcccucgagugcaaaggcagaagggagcuu
gacugcaagacccacccgucgagcagggacgaaagucggccuuagugauc
cgacggugccgaguggaagggccgucgcucaacggauaaaaguuacucua
gggauaacaggcugaucuuccccaagaguucacaucgacgggaagguuug
gcaccucgaugucggcucuucgccaccuggggcuguaguauguuccaagg
guugggcuguucgcccauuaaagcgguacgugagcuggguucagaacguc
gugagacaguucgguccauauccggugugggcguuagagcauugagagga
ccuuucccuaguacgagaggaccgggaaggacgcaccucugguguaccag
uuaucgugcccacgguaaacgcuggguagccaagugcggagcggauaacu
gcugaaagcaucuaaguaguaagcccaccccaagaugagugcucuccuau

..............<<<<<<<<<<.....<<..<<<<<<<<<<<.<....
..<<<<<<.....((.>>>.....<<<<<<<..<<.))......>>....
.>>>>>>>...>>>....<<<....>>>......<<.<<<<<........
.>>>>>...>>.>....<<<<<<.....<<....>>......>>>>>.>.
........<<....>>..<<<<<<.....<<.....>>....>>>>>>..
<<<....<<<......>>>......<<<.<<...<<<<.<<<...<<.<<
.....>>.>>((......<<<.....))>>>...>>>...>>>>....>>
...>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<
<<<>>>>>..>>>......>>.>>>>>>>.>>...............<<.
...>>....>>.........<<<<....>>>>..................
>>>>>>>>>>........<<<<..<<<<.......>>>>..>>>>...<.
<........>.>.<<<<<<....<<<<<<<<<<<<...<<<...<<....
...>>...>>>...<<....>>..<<<<.....>>>>.....>>>>>>>>
>>>>..<<.<...<<<<<<.....<.<<<<<<<..<<<<...<<<<<<..
....>>>>>>...>.>>>...<<<.<<<<<........>>>>>>>>....
>>>>>>>.>...<<<.....>>>......>>>>>>......>.>>..<<<
<<<....<<<<<....>>>>><<.<<<<<<<....<<<<<<.....<<<.
..<<<<<<<<<..<<<<<<<....>>>>>.>>..>>>>>>>>>..>>.>.
....>>>>>>..<<<<....>>>>..>>>>>>>..>>..<<<<<<<<<<.
.....>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<<.<<<.......<.<<<.
<.....<<.........>>.....>.........<<......>>...>>>
.>...>>>.>>>>>>.>>..........))).....>>>>>>.>>>...>
>>>>>><<<<........>>>>....>>>>>><.<<<<<<..........
.<..<..<<....>>.>...>.......>>>>>>..>.....>>>>>><.
.....<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...
<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<
....>>>...>>>...>>...<<<<<........>>>>>))<<<<<.<<<
<<<<<<.<<<<....<<<<..<<<..<<<<<<<<<<.....(((..>>>>
><...<<<<<...<<<....<<<<<.......>>>>>...>>>..>>>>>
....><..<<<<<....>>>>>...>>>>>>...>>>...>>>>......
...>>>>...>>>>...>>>>>..>>>>>>>>>..>>.....<<......
>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<..
.............<<<<<.....<..>......>>>>><<<<<<<.....
>>>>>>>............<<<<<<<<<..<<<.........>>>..<<<
<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<
<<..<<<...<<..<<<<<<..<<<<....>>>>...>>>>>>..>>...
>>>>>>>>..>>>>><<<<<..>>>>>........<...........<<<
<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>
>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<
<<<.<<<..<......<<<<.<<<<<<..<<<<<..<<<<<<<..<<.<<
<.<<<<<<<<<...........<<<<...<<<......<<<<<<<<....
>>>>>>>>...>>>.............>>>>..>>>>>>>>>.>>>.>>.
..<<<<<.<<<..........>>>>>>>>.....>>>>>>>...>>>>>.
.<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<
<..<<<<<<<.......>>>>>>>....<<...(((>>....>>>>>>>.
..<<<<..<<<......>>>..>>>>.<<<....>>>.>>))).......
<<<<<<<.<<..>>>>..>>>>>>>>>.............>>>>..>>>>
>>.......<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>
>>.>.......<<<<<.<.<<<<..<<<<<<<<........>>>>>..>>
>.<<<<<.....>>>>>.....>>>>...>...>>>.>>....<<<<<<<
....>>>.>>>>....>...>>>>>>>>>>>....<<<<<<<...<.<<.
.<<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<
<<<<<<<))).>>>>>>...>>>>>...>>>>.>>>>>..<.<<...<<<
<<<...........>>>>>>...>>>.>>.>.......>>>>>>>.....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mlc Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): E40 R42 I43 K45 R99 N102 Q103 M104 G106 L107 F149 S150 K178 S179 G182 Q183 Y197 K198 K200 K215
• Binding residue (residue number reindexed from 1): E1 R3 I4 K6 R60 N63 Q64 M65 G67 L68 F110 S111 K139 S140 G143 Q144 Y158 K159 K161 K176

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mlc, PDBe:5mlc, PDBj:5mlc
• PDBsum: 5mlc
• PubMed: 27986857
• UniProt: P82193|RK6_SPIOL Large ribosomal subunit protein uL6c (Gene Name=RPL6)