Structure of PDB 5hd1 Chain 28 Binding Site BS01

Receptor Information

>5hd1 Chain 28 (length=64) Species: 300852 (Thermus thermophilus HB8)

PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPYE

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): P2 K3 M4 K5 T6 H7 K8 K12 R13 K15 T17 A18 S19 K21 K26 T27 K29 R30 H31 L32 N33 W34 Q35 K39 I41 R42 Q43 K44 R46 K47 F48 A51 K52 E54 R57 L60 P63 Y64
• Binding residue (residue number reindexed from 1): P1 K2 M3 K4 T5 H6 K7 K11 R12 K14 T16 A17 S18 K20 K25 T26 K28 R29 H30 L31 N32 W33 Q34 K38 I40 R41 Q42 K43 R45 K46 F47 A50 K51 E53 R56 L59 P62 Y63

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: Q5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)