Structure of PDB 7ood Chain a Binding Site BS01

Receptor Information

>7ood Chain a (length=285) Species: 272634 (Mycoplasmoides pneumoniae M129)

PIKKIISRSNSGIHHSTVIDYKKLLTTNKNKPEKSLLVTLKKHGGRNNQG
KITVRHQGGRNKRKYRIIDFKRTHYDNIEATVKSIEYDPNRSCFVSLITY
ANGAKSYIISPDGIKVGDKILASEHPIDIKPGFSMPLAFIPEGTQVHNIE
LHPKGGGQIARSAGSYARILGQDETGKYVILQLLSGETRKFLKECRATVG
VVSNLDHNLVVIGKAGRNRHRGIRPTVRGSAMNPNDHPHGGGEGRSPVGR
DAPRTPWGKRHMGVKTRNMKKASTNLIIRNRKGEQ

Ligand information

>7ood Chain 3 (length=2879)

aguuacuaagggcuuaugguggaugccuuggcacuaauaggcgaugaagg
acguguuaaccugcgauaagcuucggguaggugguaagaaccucagaucc
ggagauuuccgaauggagcaauccgguaguuggaaacagcuaucauuaau
ugaugaauaaauagucaauuaaagcaauacguggugaagugaaacaucuc
aguagccacaggaaaagaaaacgaaugugauuccguguguaguggcgagc
gaaagcggaacaggccaaacuuaucauuagauagggguuguagggcuugc
aauguggacuugaaaacgauagaagaagcuguuggaaagcagcgcgcaaa
agggugauagccccguauuugaaauuguuuucauaccuagcgagaucccu
gaguagcucggaaaacguuauuuugagugaaucugcccagaccauugggu
aagccuaaauacuaauuagugaccgauagcgaaacaguaccgugagggaa
aggugaaaagaacccagagaugggagugaaauagauucugaaaccauaug
ccuacaacgugucagagcacauuaaugugugauggcgugcguuuugaagu
augagccggcgaguuaugauagcaagcguuaguuaaccaggagaugggga
gcuguagcgaaagcgaguuuuaaaagagcguuuguuuguuauuauagacc
cgaaacggguugagcuagucaugagcagguugaagguugaguaacaucaa
cuggaggaccgaaccgacucucguugaaacgauagcggaugacuugugau
uaggggugaaauuccaaucgaaauccgugauagcugguucucgucgaaau
agcuuuaaggcuagcgugagaucacaaauaaguggagguaaagcuacuga
auguaugauggcgccaccuaggcguacugaauacaauuaaacucugaaug
ccauuuauuuuauucucgcagucagacagugggggauaagcuucauuguc
aagaggggaagagcccagaucauuaaauaagguccccaaaauauacuaag
uggaaaaggaugugaaagugcuaaaacagcaaggauguuggcuuagaagc
agccaucguuuaaagagugcguaacagcucacuugucgaguguuuuugcg
ccgaagauguaacggggcuaaguauauuaccgaauuuauggauaagauuu
auaucuugugguagacgagcguuguauuggaguugaagucaaagcgugag
cauugguggauccaauacaagugagaaugccggcaugaguaacgcuuggg
agugagaaucucccaaaccgauugacuaagguuuccuggaccagggucgu
ccuuccaggguuagucuggaccuaagcugaggcugaaaagcguaggcgau
ggacaacagguuaauauuccuguacuuacaguuagacugauggagugaca
aagaagguuuuccacccccauaauuggauuuggggauaaaucauaaggug
guacaauaggcaaauccguugugcauaacauugagugaugaugucgagug
aaaguagcgaaggugguauuaaucaugcuuucaagaaaagcuucuagggu
uaaucuagcuguaaccaguaccgagaacgaacacacguagucaaggagag
gauccuaagguuagcgagugaacuauagccaaggaacucugcaaauuaac
cccguaaguuagcgagaaggggugcuuauguaaaaguaagccgcagugaa
gaacgaggggggacuguuuaacuaaaacacaacucuaugccaaaccguaa
ggugauguauauggggugacaccugcccagugcuggaagguuaaagaagg
agguuagcgcaagcgaagcuuuuaacugaagccccagugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuagucggguaaauuccgu
cccgcuugaaugguguaaccaucucuugacugucucggcuauagacucgg
ugaaauccagguacgggugaagacacccguuaggcgcaacgggacggaaa
gaccccgugaagcuuuacuguagcuuaauauugaucaggacauuaucaug
uagagaauagguaggagcaaucgaugcaaguucgcuaggacuuguugaug
cgaaagguggaauacuacccuugguugugugcuguucuaauugguaacug
uuauccaguuucaagacaguguuaggugggcaguuugacuggggcggucg
ccuccuaaaagguaacggaggcguacaaagguaccuucaguacgguugga
aaucguauguagaguguaaugguguaagggugcuugacugugagacauac
aggucgaacaggugagaaaucaggucauagugauccggugguccaguaug
gaauggccaucgcucaacggauaaaagcuacuccggggauaacaggcuga
uacugcccaagaguucauaucgacggcaguguuuggcaccucgaugucga
cucaucucauccucgagcugaagcagguucgaaggguucggcuguucgcc
gauuaaagagauacgugaguuggguucaaaccgucgugagacagguuggu
cccuaucuauugugcccguaggaagauugaagaguguugcuucuaguacg
agaggaccgaagcgaggacaccucuuaugcuccaguuguagcgccagcug
caccgcuggguaguaacgugucuauuagauaaacgcugaaagcaucuaag
ugugaaacuaucucaaagauuaaucuucccauuucgaaaguaagagccgu
caaagacgaugacguugauagguuacagguguaagcauagugauauguug
agcugaguaauacuaauugcucgaggacu

<<<......<<<<.<<<<<<....{[[..[[<<<<<<<[[<<......<<
<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>.....>>>
>>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<
<<<<.........>>>>>>>>>.>>....<<<<<<.....<<....>>..
....>>>>>.>.........<<....>>..<<<<<<.....<<.....>>
....>>>>>>..(((....<<<<<......>>>>>......<<<<<<<<<
.....<....<<<<<<<<<<.<<<...<<<<<......>>>>>((.....
.<<<.....))>>>...>>>...>>>>>>>>>>...>..>>>>>..>>>>
.....<<<<<<<<.......>>>>>>>>......<<<<<..<<<<>>>>>
..)))......]].>>>>>>>.]]...............<<....>>...
.]].........<<<<....>>>>.............}....>>>>>>.>
>>>.......<<<<..<<<<......>>>>..>>>>...<<<........
>>>.<<<<<<....<<<<<<<<<<<<<...<<<...<<<.....>>>...
>>>...<<....>>..<<<<.....>>>>....>>>>>>>>>>>>>..<<
.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>
>>.....>>>...<<<.<<.<<........>>.>>>>>....>>>>>>>>
>...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<
<<<<....>>>>><<<<<<<<....<<<<<<<<<<......<<....<<.
.<<<<<...<.<<<<.....>>>>..>...>>>>>..>>..>>.......
>>>>>>>>>>...>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>
....<<<......>>>...<<<<.<<<...<<<(((...<<<<<<<....
.......<<..<<<<<<<<<<.......<<<<<.<<...<<<<.......
>>>>...>>.........<<......>>...>>>>>...>>>>>>>>>>.
>>...........))).....>>>>>>>>>>...>>>>>>><<<<<<<..
..>>>>>>>....>>>>>><<<<<<<<<<<<......<<<<<.<<....>
>.>>>>>...>>>>>>>>>>.>>.....>>>>>>.......<<...<<<<
<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...
>>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<<...<
<<<...<<<..<<<<<<<<<....(((...>>>>><<..<<<<<..<<<<
<<<<<<<.<<.....>>>>>>>>>....>>>>..>>>>>...>><..<<.
......>>...>>>>>....>>>....>>>>........>>>>>..>>..
...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>>..<<<<<...<<<<<<<<.<<...............<<
<<<.....<..>......>>>>><<<<<<......>>>>>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....
>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<..<<
<<<<..<<....>>...>>>>>>..>>...>>>>>>>>..>>>>><<<<<
<.......>>>>>>........<...........<.<<<.......>>>.
>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>>>>>>>
>...........<<<<<........>>>>>..<<<<<<<..(((.[[...
...<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<.<<<.<<<<..<<<..
.........<<<<<..<<<......<<<<<<<......>>>>>>>...>>
>.............>>>>>..>>>..>>>>.>>>.>>...<<<..<<<<<
.....>>>>>.>>>....>>>>>>>>>..>>>>>..<<<<.....>>>><
<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.....
..>>>>>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<....
..>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>>
>..))>>>>>>>.............>>>>..]]>>>>.......<<<<..
.<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<<<
<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>
>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>...
.]]..))).>>>>>>>....<<<<<<<....<<<..<<<<<<<.......
........>>>>>>><<<<<<...<<<<...<<<<<<<<<<<.)))>>>>
>>..>>>>>...>>>>.>>>>>>..<<<....<<<<<...........>>
>>>....>>>.>>>........>>>>>>>...<<..>>.....<<<<<<<
<.........>>>>....<<<<<<<<.<<<....<<<<<....>>>>>..
.>>>..>>>>>.>>>...>>>>....>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ood Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R9 S10 N11 S12 I14 H15 N31 K35 T40 K42 K43 H44 R47 N48 N49 Q50 K52 I53 T54 V55 R56 H57 Q58 G60 N62 K63 R64 K65 Y66 K84 Y88 R92 T100 N103 G104 L152 H153 P154 K155 Q159 A161 R162 S163 A164 G165 S166 Y179 L185 S186 E188 R190 L193 L206 H208 N209 I213 K215 A216 G217 R218 N219 R220 H221 R225 P226 T227 V228 R229 G230 S231 A232 M233 N234 N236 D237 H240 G242 E244 G245 R246 P248 V249 G250 R251 D252 P254 R255 P257 W258 G259 R261 H262 M263 G264 K266 T267 R268 K271 S274 R282
• Binding residue (residue number reindexed from 1): R8 S9 N10 S11 I13 H14 N30 K34 T39 K41 K42 H43 R46 N47 N48 Q49 K51 I52 T53 V54 R55 H56 Q57 G59 N61 K62 R63 K64 Y65 K83 Y87 R91 T99 N102 G103 L151 H152 P153 K154 Q158 A160 R161 S162 A163 G164 S165 Y178 L184 S185 E187 R189 L192 L205 H207 N208 I212 K214 A215 G216 R217 N218 R219 H220 R224 P225 T226 V227 R228 G229 S230 A231 M232 N233 N235 D236 H239 G241 E243 G244 R245 P247 V248 G249 R250 D251 P253 R254 P256 W257 G258 R260 H261 M262 G263 K265 T266 R267 K270 S273 R281

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7ood, PDBe:7ood, PDBj:7ood
• PDBsum: 7ood
• PubMed: 36171285
• UniProt: P75577|RL2_MYCPN Large ribosomal subunit protein uL2 (Gene Name=rplB)