Structure of PDB 8d8l Chain 0 Binding Site BS01

Receptor Information
>8d8l Chain 0 (length=447) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELRLLSKTLQGQSYRDQLELNPDVSKAINNNIMAVHIPNNLRRVATNYYK
EIQEPNSLHRPCRTKMEVDAHIASIFLQNYGSIFQSLKELQKRVGPDNFK
PQRILDVGYGPATGIVALNDILGPNYRPDLKDAVILGNAEMQERAKIILS
RQLIMTNLRSSIPASKEYDLIILTHQLLHDGNQFPIQVDENIEHYLNILA
PGGHIVIIERGNPMGFEIIARARQITLRPENFPDEFGKIPRPWNYFLKVI
APCPHQRKCPLQVGNPNFYTHKEGKDLKFCNFQKSIKRPKFSIELKKGKL
LATSWDNGRDYEILNYSYLIFERSHKDENTLKEIKKLRNENVNGKYDIGS
LGDDTQNSWPRIINDPVKRKGHVMMDLCAPSGELEKWTVSRSFSKQIYHD
ARKSKKGDLWASAAKTQIKGLGDLNVKKFQLKKEERQKARKAMESYN
Ligand information
>8d8l Chain a (length=1506) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaagaauaugauguugguucagauuaagcgcuaaauaaggacaugacaca
ugcgaaucauacguuuauuauugagauaauaaauaugugguguaaacgug
aguaauuuuauuaggaauuaaugaacuauagaauaagcuaaauacuuaau
auuauauaaaaauaauuuauauaauaaaaaggauauauauauauauauuu
aucuauagucaagccaauaaugguuuagguaguagguuuauuaagaguua
aaccuagccaacgauccauaaucgauaaugaaaguuagaacgaucacguu
gacucugaaauauagucaauaucuauaagauacagcagugaggaauauug
gacaaugaucgaaagauugauccaguuacuuauuaggaugauauauauau
auauauaaauugauuaaaaauaaaauccauaaauaauuaaaauaaugaua
uuaauuaccauauauuuauauggauauauauauauuuuaauaguccugac
uaauauuugugccagcagucgcgguaacacaaagagggcgagcguuaauc
auaaugguuuaaaggauccguagaaugaauuauauauaauuuagaguuaa
uaaaauauaauuaaagaauuauaauaguaaagaugaaauaauaauaauaa
uuauaagacuaauauaugugaaaauauuaauuaaauauuaacugacauug
agggauuaaaacuagaguagcgaaacggauucgauacccguguaguucua
guaguaaacuaugaauacaauuauuuauaauauauauauaaauaauaaau
gaaaaugaaaguauuccaccugaagaguacguuagcaauaaugaaacuca
aaacaauagacgguuacagacuuaagcaguggagcauguuauuuaauucg
auaauccacgacuaaccuuaccauauuuugaauauuauaauaauuauaau
uauuauauuacaggcguuacauuguugucuuuaguucgugcugcaaaguu
uuagauuaaguucauaaacgaacaaaacuccauauauauaauuuuaauua
uauauaauuuuauauuauuuauuaauauaaagaaaggaauuaagacaaau
cauaaugauccuuauaauauggguaauagacgugcuauaauaaaaugaua
auaaaauuauauaaaauauauuuaauuauauuuaauuaauaauauaaaac
auuuuaauuuuuaauauauuuuuuuauuauaauaugaauuauaaucugaa
auucgauuauaugaaaaaagaauugcuaguaauacguaaauuaguauguu
acggugaauauucuaacuguuucgcacuaaucacucaucacgcguugaaa
cauauuauuaucuuauuauuuauauaauauuuuuuaauaaauauuauuaa
uuuauauuuauuuauaucagaaauaauaugaauuaaugcgaaguugaaau
acaguuaccguaggggaaccugcggugggcuuauaaauaucuuaaauauu
cuuaca
...<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<......<<<.
<<<..<<<..<<<<<<<<<<<<..>>>>>>>>>>..>>>>>.....<<<.
.......<<<<<.<<.........<<<<<<<<.<<<<.......>>>>..
.<<<<<<<<<.....>>>>>>>>>......<<<<<<<<<..>>>>>>>>>
.>>>>>>>>....>>>>>>><<<....<<<..<<<<<<<<........>>
>>>>>>>>>......>>>..<<<<.<<<<....>>>>...>>>>.>>><<
<<<<.........>>>>>><<<<.....>>>>..>>>>>>.........<
<<...<<<<<....>>>>.>>>>...>.>>>>>>.<<<<..<<<<<<...
.>>>>>>..<<......>>.....>>>>..<<<<<<<<............
..>>>>><<<<<<<..>>>>>>>.<<<<..>>>>.>>>....<<<<<(((
.....<<<<.....<<.)))>>.......>>>>.>>>>>..>>>>>>>>>
.....<<<((.....<<<<...<.<<.<<<<<<..>>>>>>...<<<<<<
<<.....<<<<<<<<<..<<<<<<<....<...........>.......>
>>>>>>..>>.......<<....>>.>>>>>>>..>>>>>>>>...>>>.
..>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...>>>>>>
>>..........<<<<<<.<<<<<<<<<<<<..>>.>>>>>>>>>>..<<
..))>>....>>>>>>.>>>.<<.......<<<<....>>>>.....>>.
.)))).]<<.<<...<<<<......<<<<<..<<<<<<<<<<........
....................<<<<<<<.....<<.<<<<<<<<<<..>>>
>>>>>>>.>>.<<<.<<..<<<<<<<<<<<<..<<<<<<<<<....>>>.
...<<......>>....>>>>>>.....<<<.<<<<<<<<........>>
>>>>>>..<<<<<<<<<.....>>>>>>>>>....>>>...>>>>>>>..
..>>>>>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<...
.....<<<..<<..<<<<<<......>>>>>>..>>....>>>......>
>>>>>......<<<<<.<....>.>>>>>.....<....<<<<<<<....
....>>>>>>>....>.....>>>>>.....<<.<<<<<.........>>
>>>>>...........>>>>..>>..>>....<.<<<.<.<<<<<<<<..
<<<<<<<<<.<<<...<<<..<<<.<<<<<...<<<<<<<...>>>>>>>
...>>>>>>>>..>>>..>>>>>>>>>>>>..>>>>>>>>..>.>>.>.>
.....<<<<<<<<<....>>>>>>>>>.......................
......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8d8l Principles of mitoribosomal small subunit assembly in eukaryotes.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
Y109 Q113 R123 I135 Q138 H280 D281 Q284 I287 Q288 R311 N313 P314 T390 H391 K392 K395 K398 R408 K416 K419 L421 T423 S424 W425 N442 G443 R444 D445 Y446 N450 I498 N499 D500 R504 K505 H507 M509 D511 K521 R526 R537 K538 L575 K576 K577 R580 Q581 R584 K585
Binding residue
(residue number reindexed from 1)
Y49 Q53 R63 I75 Q78 H179 D180 Q183 I186 Q187 R210 N212 P213 T270 H271 K272 K275 K278 R288 K296 K299 L301 T303 S304 W305 N307 G308 R309 D310 Y311 N315 I363 N364 D365 R369 K370 H372 M374 D376 K386 R391 R402 K403 L431 K432 K433 R436 Q437 R440 K441
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008168 methyltransferase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006412 translation
GO:0032543 mitochondrial translation
GO:0180026 mitochondrial small ribosomal subunit assembly
Cellular Component
GO:0005739 mitochondrion
GO:0005763 mitochondrial small ribosomal subunit

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8d8l, PDBe:8d8l, PDBj:8d8l
PDBsum8d8l
PubMed36482135
UniProtP36056|RT22_YEAST Ribosome assembly protein RSM22, mitochondrial (Gene Name=RSM22)

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