Structure of PDB 6swd Chain E Binding Site BS01

Receptor Information

>6swd Chain E (length=242) Species: 272844 (Pyrococcus abyssi GE5)

ARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRD
YLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYR
VLPNRIGKLILHPISEEEANIKPLRIRNKRMVKGAKIQLNFHDGTNHLIP
LSEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVE
IKKFPMGWPDVVTIEDEEGELFDTLKEYAFVVGRDKPRISLP

Ligand information

>6swd Chain 2 (length=1044)

auuccgguugauccugccggaggccacugcuauggggguccgacuaagcc
augcgagucaagggggcgucccuucugggacgccaccggcggacggcuca
guaacacgucgguaaccuacccucgggagggggauaaccccgggaaacug
gggcuaaucccccauaggccugggguacuggaagguccccaggccgaaag
ggagccguaaggcuccgcccgaggaugggccggcggccgauuagguaguu
ggugggguaacggcccaccaagccgaagaucgguacgggccgugagagcg
ggagcccggagauggacacugagacacggguccaggcccuacggggcgca
gcaggcgcgaaaccuccgcaaugcgggaaaccgcgacggggggaccccca
gugccgugccucuggcacggcuuuuccggaguguaaaaagcuccgggaau
aagggcugggcaaggccgguggcagccgccgcgguaauaccggcggcccg
agugguggccacuauuauugggccuaaagcggccguagccgggcccguaa
gucccuggcgaaaucccacggcucaaccguggggcucgcuggggauacug
cgggccuugggaccgggagaggccggggguacccccgggguaggggugaa
auccuauaaucccggggggaccgccaguggcgaaggcgcccggcuggaac
ggguccgacggugagggccgaaggccaggggagcgaaccggauuagauac
ccggguaguccuggcuguaaaggaugcgggcuaggugucgggcgagcuuc
gagcucgcccggugccguagggaagccguuaagcccgccgccuggggagu
acggccgcaaggcugaaacuuaaaggaauuggcgggggagccugcuccuu
gcacacaccgcccgucacuccacccgagcggggccuaggugaggcccgau
cuccuucgggaggucgggucgagccuaggcuccgugaggggggagaaguc
guaacaagguagccguaggggaaccuacggcucgaucaccuccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6swd Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R3 K4 G5 P6 R8 H9 R12 L13 K24 Y26 W28 A29 V30 R31 P34 Y47 R50 R60 K64 R76 Y81 K82 K130 M132 A136 Q139 G145 N147 K155 K191 F205 M207 G208 W209 D224
• Binding residue (residue number reindexed from 1): R2 K3 G4 P5 R7 H8 R11 L12 K23 Y25 W27 A28 V29 R30 P33 Y46 R49 R59 K63 R75 Y80 K81 K129 M131 A135 Q138 G144 N146 K154 K190 F204 M206 G207 W208 D223

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6swd, PDBe:6swd, PDBj:6swd
• PDBsum: 6swd
• PubMed: 32029867
• UniProt: Q9V1U8|RS4E_PYRAB Small ribosomal subunit protein eS4 (Gene Name=rps4e)