Structure of PDB 5mlc Chain S Binding Site BS01

Receptor Information

>5mlc Chain S (length=116) Species: 3562 (Spinacia oleracea)

TRVKRGYIARRRRKKIRFFASSFRGAHSRLTRTIAQQKIRALVSAHRDRD
RQKRDFRRLWITRINAAIRERGVYYNYSKFIHDLYKRQLLLNRKILAQIA
ILNPNCIYMIYNEIIK

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): T2 R3 V4 K5 R6 G7 Y8 I9 R11 R12 R13 R14 K15 R18 S22 F24 R25 G26 A27 H28 R30 L31 T32 R33 Q37 Q38 R41 A42 S45 A46 R48 D49 D51 R52 Q53 K54 R55 F57 R58 R59 I62 N66 R70 N77 Y78 S79 H83 Y86 N93 R94 K95
• Binding residue (residue number reindexed from 1): T1 R2 V3 K4 R5 G6 Y7 I8 R10 R11 R12 R13 K14 R17 S21 F23 R24 G25 A26 H27 R29 L30 T31 R32 Q36 Q37 R40 A41 S44 A45 R47 D48 D50 R51 Q52 K53 R54 F56 R57 R58 I61 N65 R69 N76 Y77 S78 H82 Y85 N92 R93 K94

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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: P28803|RK20_SPIOL Large ribosomal subunit protein bL20c (Gene Name=rpl20)