Structure of PDB 6gzz Chain K2 Binding Site BS01

Receptor Information

>6gzz Chain K2 (length=150) Species: 300852 (Thermus thermophilus HB8)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Ligand information

>6gzz Chain A2 (length=2912)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccga
aaaguccgcggccguggacccgaaaccgggcgagcuagcccuggccaggg
ugaagcuggggugagacccaguggaggcccgaaccggugggggaugcaaa
ccccucggaugagcuggggcuaggagugaaaagcuaaccgagcccggaga
uagcugguucuccccgaaaugacuuuagggucagccucaggcgcugacug
gggccuguagagcacugauagggcuagggggcccaccagccuaccaaacc
cugucaaacuccgaagggucccagguggagccugggagugagggcgcgag
cgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaagg
cccccaagucugggcuaagugguaaaggauguggcgccgcgaagacagcc
aggauguuggcuuagaagcagccaucauuuaaagagugcguaauagcuca
cuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgcc
gaagcugcgggucugggggaugaccccaggcgguaggggagcguucccga
ugccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcga
augccggcaugaguaacgauaaagagggugagaaucccucucgccguaag
cccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccua
aggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcc
cuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagcc
auggacgagcccggccagaagcgcagggugggagguaggcaaauccgccu
cccaacaagcucugcgugguggggaagcccguacgggugacaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gzz Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
• Resolution: 4.13 Å
• Binding residue (original residue number in PDB): R7 P8 A12 N13 K14 R15 R16 K17 R18 R21 G22 P23 G24 G26 H27 K29 T30 A31 T32 R33 H35 K36 G37 Q38 K39 S40 R41 S42 G43 K46 D47 P48 R49 R50 F51 E52 G53 R55 T58 R61 L62 P63 K64 G66 M67 Q68 Q70 V71 P72 G73 I75 R77 Y80 Q81 G82 K107 K113 L115 G116 E117 E119 K132 S133
• Binding residue (residue number reindexed from 1): R7 P8 A12 N13 K14 R15 R16 K17 R18 R21 G22 P23 G24 G26 H27 K29 T30 A31 T32 R33 H35 K36 G37 Q38 K39 S40 R41 S42 G43 K46 D47 P48 R49 R50 F51 E52 G53 R55 T58 R61 L62 P63 K64 G66 M67 Q68 Q70 V71 P72 G73 I75 R77 Y80 Q81 G82 K107 K113 L115 G116 E117 E119 K132 S133

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gzz, PDBe:6gzz, PDBj:6gzz
• PDBsum: 6gzz
• PubMed: 30301898
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)