Structure of PDB 5hd1 Chain 2m Binding Site BS01

Receptor Information
>5hd1 Chain 2m (length=116) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAE
VVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQR
TRTNARTRKGPRKTVA
Ligand information
>5hd1 Chain 2a (length=1483) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcgggguacuccguggucagcggcggacggg
ugaguaacgcgugggugaccuacccggaagagggggacaacccggggaaa
cucgggcuaaucccccauguggacccgccccuugggguguguccaaaggg
cuuugcccgcuuccggaugggcccgcgucccaucagcuaguugguggggu
aauggcccaccaaggcgacgacggguagccggucugagaggauggccggc
cacaggggcacugagacacgggccccacuccuacgggaggcagcaguuag
gaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggagga
agaagcccuucgggguguaaacuccugaacccgggacgaaacccccgacg
aggggacugacgguaccgggguaauagcgccggccaacuccgugccagca
gccgcgguaauacggagggcgcgagcguuacccggauucacugggcguaa
agggcguguaggcggccuggggcgucccaugugaaagaccacggcucaac
cgugggggagcgugggauacgcucaggcuagacggugggagaggguggug
gaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccgau
ggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcgug
gggagcaaaccggauuagauacccggguaguccacgcccuaaacgaugcg
cgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgcgc
cgccuggggaguacggccgcaaggcugaaacucaaaggaauugacggggg
cccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaac
cuuaccaggccuugacaugcuagggaacccgggugaaagccugggccuag
cacaggugcugcauggccgucgucagcucgugccgugagguguuggguua
agucccgcaacgagcgcaacccccgccguuaguugccagcgguucggccg
ggcacucuaacgggacugcccgcgaaagcgggaggaaggaggggacgacg
ucuggucagcauggcccuuacggccugggcgacacacgugcuacaaugcc
cacuacaaagcgaugccacccggcaacggggagcuaaucgcaaaaaggug
ggcccaguucggauuggggucugcaacccgaccccaugaagccggaaucg
cuaguaaucgcggaucagccaugccgcggugaauacguucccgggccuug
uacacaccgcccgucacgccaugggagcgggcucuacccgaagucgccgg
gagccuacgggcaggcgccgaggguagggcccgugacuggggcggucgua
acaagguagcuguaccggaaggugcggcuggau
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<
<.<<<..<<<..<<.<<<<<<<<<....>>>>>>>>>.>>>>>......<
<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<.....
.>>>>>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<
<...>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<..
.....>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>
.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>.
.......<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<..
....<<<<....>>>>.....>>>>....<<<<<......<.<<<<....
.>>>>..>.......>>>>>......<<<<<(((...<<<<<.....<<.
)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<((..
...<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>
>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<.
...<<<<<<<.<..<<<......>>>.....>.>>>>>>>..........
.<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<
<...<<...<<<<.<.....>.>>>>...>>>>>>>>..........<<<
<<<..<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>
.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<
<<<<.<<.<<<<<<..<<<<<<<<<<......<<........>>......
....<<<<<<<......<<<<<<<...<<<<<<<....>>>>>>>>>>>>
>>..<<.<<<..<<<<<<.......<<<<<<<<<....>>>..<<<<...
...>>>>..>>>>>>.....<<<<.<<<<<<<..<<<..<<<.....>>>
>>>...>>>>>>>.....<<<<<....>>>>>........>>>>......
...>>>...>>>>>>>>....>>>>>>>...>>.>>>>>>>>.....<<<
<<<<.....<<<..<<..<<<<....>>>>..>>....>>>.....>>>>
>>>......<....<<<<<<<........>>>>>>>....>.....>>>>
>>....<<<<<<<..........>>>>>>>......>>...>>>>>>>>>
>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<<<<...<.<<<<..
..<<<....>>>.>>>>.>..>>>>>>>>>>>>>..>>>.>>>>>.>>..
.>.....<<<<<<<<<....>>>>>>>>>....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5hd1 Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		R14 Y21 Y23 G24 I25 G26 A28 R29 R44 N77 Y87 R88 R91 H92 V98 R99 Q101 R102 T103 R104 T105 N106 A107 R108 T109 K111 R114 K115 T116
Binding residue
(residue number reindexed from 1)		R12 Y19 Y21 G22 I23 G24 A26 R27 R42 N75 Y85 R86 R89 H90 V96 R97 Q99 R100 T101 R102 T103 N104 A105 R106 T107 K109 R112 K113 T114
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5hd1, PDBe:5hd1, PDBj:5hd1
PDBsum5hd1
PubMed26809677
UniProtP80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)

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