Structure of PDB 6vmi Chain K Binding Site BS01

Receptor Information

>6vmi Chain K (length=177) Species: 9606 (Homo sapiens)

SSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALS
DCGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPV
AIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPEDILKNLVEELPQPRKI
PKRLDEYTQEEIDAFPRLWTPPEDYRL

Ligand information

>6vmi Chain A (length=1527)

gcuaaaccuagccccaaacccacuccaccuuacuaccagacaaccuuagc
caaaccauuuacccaaauaaaguauaggcgauagaaauugaaaccuggcg
caauagauauaguaccgcaagggaaagaugaaaaauuauaaccaagcaua
auauagcaaggacuaaccccuauaccuucugcauaaugaauuaacuagaa
auaacuuugcaaggagagccaaagcuaagacccccgaaaccagacgagcu
accuaagaacagcuaaaagagcacacccgucuauguagcaaaauaguggg
aagauuuauagguagaggcgacaaaccuaccgagccuggugauagcuggu
uguccaagauagaaucuuaguucaacuuuaaauuugcccacagaacccuc
uaaauccccuuguaaauuuaacuguuaguccaaagaggaacagcucuuug
gacacuaggaaaaaaccuuguagagagaguaaaaaauuuaacacccauag
uaggccuaaaagcagccaccaauuaagaaagcguucaagcucaacaccca
cuaccuaaaaaaucccaaacauauaacugaacuccucacacccaauugga
ccaaucuaucacccuauagaagaacuaauguuaguauaaguaacaugaaa
acauucuccuccgcauaagccugcgucagauuaaaacacugaacugacaa
uuaacagcccaauaucuacaaucaaccaacaagucauuauuacccucacu
gucaacccaacacaggcaugcucauaaggaaagguuaaaaaaaguaaaag
gaacucggcaaaucuuaccccgccuguuuaccaaaaacaucaccucuagc
aucaccaguauuagaggcaccgccugcccagugacacauguuuaacggcc
gcgguacccuaaccgugcaaagguagcauaaucacuuguuccuuaaauag
ggaccuguaugaauggcuccacgaggguucagcugucucuuacuuuuaac
cagugaaauugaccugcccgugaagaggcgggcauaacacagcaagacga
gaagacccuauggagcuuuaauuuauuaaugcaaacaguauaccaaaccu
gcauuaaaaauuucgguuggggcgaccucggagcagaacccaaccuccga
gcaguacaugcuaagacuucaccagucaaagcgaaccucaauugauccaa
uaacuugaccaacggaacaaguuacccuagggauaacagcgcaauccuau
ucuagaguccauaucaacaauaggguuuacgaccucgauguuggaucagg
acaucccgauggugcagccgcuauuaaagguucguuuguucaacgauuaa
aguccuacgugaucugaguucagaccggaguaauccaggucgguuucuau
cuacuuucaaauuccucccuguacgaaaggacaagagaaauaaggccuac
uucacaaagcgccuucccccguaaaugauaucaucucaacuuaguauuau
acccacacccacccaagaacaggguuu

<<<.......<<<<....................................
.<......>.........<.....<<.....>>....>........>>.>
>.............<<....>>......................>>>...
........<<<.......>>>...<.<........>.>.<<<<<<.....
....<<<.<<..<<....>>...>>.>>>...<<.<..<<<<<.<.....
<<<<<.<<<..<<.......>>...<<<..<<<<........>>>>.>>>
....>>>.>>>>>...<<.......>>......>.>>>>...>..>.>>.
.<<<<<<....<<<<....>>>><<<.<<<<<<<<<<.....<<......
....>>.....>>>>>>>>>>..>>>.<<<<<<<<<<......>>>>>>>
>>>...<<<......>>>....<<<.<<<...<..............<..
...<<.........>>.....>.......<<<......>>>.........
...........................>...>>>>>>........>>>>>
>...<<<<<......>>>>>.........>>>>>><......<<..<<<.
...>>><<<<..<<<<........<<<<<..............>>>>>..
....<<<...<<<<.......................>>>>.......>>
>.....<<......>>.>>>>.....>>>>..<<<<...<<<<<<<<.<<
................<<<<<<..<<<.........>>>...<<<<<<..
...........>>>>>>....<<<.<<<..<<<<<....>>>..>>>>><
<<<<<......>>>>>>........<...........<<<<<<.....>>
>>>>.....>....>>>....>>.>>>>........>>.>>>>>>>>>>>
>.>>.....>.....<<<<<........>>>>>.......<<..<<<.<<
......<<<<.<<<<<<..<<<<..<<<<<<<<.....<..>.......>
>>>>>>>.>>>>..<<<<.....>>>><<<<<<...........>>>>>>
..<......<<<..<<<<.....>>>>..>>>.....>.........<<<
....>>>............>>>>..>>>>>>.......<<<...<<<<<<
<...<<.......>>...>>>>>>>....>>.>.......<.<<<.<<<<
<<..<<.<<<<<<......>>>>>>...>>.<<<<<.....>>>>>....
.>>>>>..>...>>>..>....<<<<<<<....>>>.>>>>....>>..>
>>.>>...<.<<<.<<<.................>>>.>>><<<<<...<
<<....>>>.>>>>>......<<<................>>>......>
..........<<<<.......>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vmi Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): G29 K30 A49 L50 S68 K71 K75 S78 H80 Y83 F87 L97 R98 Y109 M111 K114 N115 L116 H117 R118 R119 Y176 R177
• Binding residue (residue number reindexed from 1): G28 K29 A48 L49 S67 K70 K74 S77 H79 Y82 F86 L96 R97 Y108 M110 K113 N114 L115 H116 R117 R118 Y175 R176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005761 mitochondrial ribosome
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6vmi, PDBe:6vmi, PDBj:6vmi
• PDBsum: 6vmi
• PubMed: 32737313
• UniProt: Q9BYD1|RM13_HUMAN Large ribosomal subunit protein uL13m (Gene Name=MRPL13)