Structure of PDB 6vmi Chain AX Binding Site BS01

Receptor Information

>6vmi Chain AX (length=353) Species: 9606 (Homo sapiens)

RAISRTNENDPAKHGDQHEGQHYNISPQDLETVFPHGLPPRFVMQVKTFS
EACLMVRKPALELLHYLKNTSFAYPAIRYLLYGEKGTGKTLSLCHVIHFC
AKQDWLILHIPDAHLWVKNCRDLLQSSYNKQRFDQPLEASTWLKNFKTTN
ERFLNQIKVQEKYVWNKRESTEKGSPLGEVVEQGITRVRNATDAVGIVLK
ELKRQSSLGMFHLLVAVDGINALWGRTTLKREDKSPIAPEELALVHNLRK
MMKNDWHGGAIVSALSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILV
SNYNPKEFESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHC
AYL

Ligand information

>6vmi Chain AA (length=944)

auagguuugguccuagccuuucuauuagcucuuaguaagauuacacaugc
aagcauccccguuccagugaguucacccucuaaaucaccacgaucaaaag
gaacaagcaucaagcacgcagcaaugcagcucaaaacgcuuagccuagcc
acacccccacgggaaacagcagugauuaaccuuuagcaauaaacgaaagu
uuaacuaagcuauacuaaccccaggguuggucaauuucgugccagccacc
gcggucacacgauuaacccaagucaauagaagccggcguaaagaguguuu
uagaucacccccaauaaagcuaaaacucaccugaguuguaaaaaacucca
guugacacaaaauagacuacgaaaguggcuuuaacauaucugaacacaca
auagcuaagacccaaacugggauuagauaccccacuaugcuuagcccuaa
accucaacaguuaaaucaacaaaacugcucgccagaacacuacgagccac
agcuuaaaacucaaaggaccuggcggugcuucauaucccucuagaggagc
cuguucuguaaucgauaaaccccgaucaaccucaccaccucuugcucagc
cuauauaccgccaucuucagcaaacccugaugaaggcuacaaaguaagcg
caaguacccacguaaagacguuaggucaagguguagcccaugagguggca
agaaaugggcuacauuuucuaccccagaaacgauagcccuuaugaaacuu
aagggucgaagguggauuuagcaguaaacuaagaguagagugcuuaguug
aacagggcccugaagcgcguacacaccgcccgucacccuccucaaguaua
cuucaaaggacauuuaacuaaaaccccuacgcauuuauauagaggagaca
agucguaacaugguaaguguacuggaaagugcacuuggacgaac

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

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): P85 K130 G131 K163 N164 T273 K279 T313 L316 F317 K318 P319 R320 S389 L390 R393
• Binding residue (residue number reindexed from 1): P40 K85 G86 K118 N119 T228 K234 T268 L271 F272 K273 P274 R275 S344 L345 R348

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0006915 apoptotic process
• GO:0032543 mitochondrial translation
• GO:0097190 apoptotic signaling pathway

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005761 mitochondrial ribosome
• GO:0005763 mitochondrial small ribosomal subunit
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6vmi, PDBe:6vmi, PDBj:6vmi
• PDBsum: 6vmi
• PubMed: 32737313
• UniProt: P51398|RT29_HUMAN Small ribosomal subunit protein mS29 (Gene Name=DAP3)