Structure of PDB 5hd1 Chain 20 Binding Site BS01

Receptor Information

>5hd1 Chain 20 (length=75) Species: 300852 (Thermus thermophilus HB8)

TRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTL
FALVDGVVEFQDRGRLGRYVHVRPL

Ligand information

>5hd1 Chain 2A (length=2790)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccauc
cuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcuuaagcccagcgccgaagcugcgggucuggggccccaggc
gguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcu
ggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggguga
gaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcg
uaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggca
gccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucua
ggcuagggggaccggagccauggacgagcccggccagaagcgcagggugg
gagguaggcaaauccgccucccaacaagcucugcgugguggggaagcccg
cgggugacaaccccccgaagccagggagccaagaaaagccucuaagcaca
accugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagag
cacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccc
cguaacuucgggagaaggggugcucccuggggugaugagccccggggagc
cgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcg
aacucguaagaggagguauagggagcgacgcuugcccggugccggaaggu
caaggggaggggugcaagccccgaaccgaagccccggugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgg
ugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaa
gaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcggc
ugggggccuaacccucggauggggggacagcgcuuggcgggcaguuugac
uggggcggucgccuccuaaaagguaacggaggcgcccaaagguccccuca
ggcgggacggaaauccgccggagagcgcaaggguagaagggggccugacu
gcgaggccugcaagccgagcaggggcgaaagccgggccuagugaaccggu
ggucccguguggaagggccaucgaucaacggauaaaaguuaccccgggga
uaacaggcugaucucccccgagcguccacagcggcggggagguuuggcac
cucgaugucggcucgucgcauccuggggcugaagaaggucccaaggguug
ggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucguga
gacaguucggucucuauccgccacgggcgcaggaggcuugaggggggcuc
uuccuaguacgagaggaccggaagggacgcaccucugguuucccagcugu
cccuccaggggcauaagcuggguagccaugugcggaagggauaaccgcug
aaagcaucuaagcgggaagcccgccccaagaugaggccucccggcagccg
guaaggacccgggaagaccacccgguggaugggccggggguguaagcgcc
gcgaggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hd1 Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): R11 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 R44 G54 R55 D56 F57 F60 F69 R74 L75 R77
• Binding residue (residue number reindexed from 1): R2 N3 R5 D6 S7 Q8 A9 K10 R11 K15 R16 Y17 E18 Q20 R23 A24 G25 N26 I27 R30 R32 G33 T34 R35 G45 R46 D47 F48 F51 F60 R65 L66 R68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5hd1, PDBe:5hd1, PDBj:5hd1
• PDBsum: 5hd1
• PubMed: 26809677
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)