Structure of PDB 7pao Chain a Binding Site BS01

Receptor Information

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

PIKKIISRSNSGIHHSTVIDYKKLLTTNKNKPEKSLLVTLKKHGGRNNQG
KITVRHQGGRNKRKYRIIDFKRTHYDNIEATVKSIEYDPNRSCFVSLITY
ANGAKSYIISPDGIKVGDKILASEHPIDIKPGFSMPLAFIPEGTQVHNIE
LHPKGGGQIARSAGSYARILGQDETGKYVILQLLSGETRKFLKECRATVG
VVSNLDHNLVVIGKAGRNRHRGIRPTVRGSAMNPNDHPHGGGEGRSPVGR
DAPRTPWGKRHMGVKTRNMKKASTNLIIRNRKGEQ

Ligand information

>7pao Chain 3 (length=2878)

aguuacuaagggcuuaugguggaugccuuggcacuaauaggcgaugaagg
acguguuaaccugcgauaagcuucggguaggugguaagaaccucagaucc
ggagauuuccgaauggagcaauccgguaguuggaaacagcuaucauuaau
ugaugaauaaauagucaauuaaagcaauacguggugaagugaaacaucuc
aguagccacaggaaaagaaaacgaaugugauuccguguguaguggcgagc
gaaagcggaacaggccaaacuuaucauuagauagggguuguagggcuugc
aauguggacuugaaaacgauagaagaagcuguuggaaagcagcgcgcaaa
agggugauagccccguauuugaaauuguuuucauaccuagcgagaucccu
gaguagcucggaaaacguuauuuugagugaaucugcccagaccauugggu
aagccuaaauacuaauuagugaccgauagcgaaacaguaccgugagggaa
aggugaaaagaacccagagaugggagugaaauagauucugaaaccauaug
ccuacaacgugucagagcacauuaaugugugauggcgugcguuuugaagu
augagccggcgaguuaugauagcaagcguuaguuaaccaggagaugggga
gcuguagcgaaagcgaguuuuaaaagagcguuuguuuguuauuauagacc
cgaaacggguugagcuagucaugagcagguugaagguugaguaacaucaa
cuggaggaccgaaccgacucucguugaaacgauagcggaugacuugugau
uaggggugaaauuccaaucgaaauccgugauagcugguucucgucgaaau
agcuuuaaggcuagcgugagaucacaaauaaguggagguaaagcuacuga
auguaugauggcgccggcguacugaauacaauuaaacucugaaugccauu
uauuuuauucucgcagucagacagugggggauaagcuucauugucaagag
gggaagagcccagaucauuaaauaagguccccaaaauauacuaaguggaa
aaggaugugaaagugcuaaaacagcaaggauguuggcuuagaagcagcca
ucguuuaaagagugcguaacagcucacuugucgaguguuuuugcgccgaa
gauguaacggggcuaaguauauuaccgaauuuauggauaagauuuauauc
uugugguagacgagcguuguauuggaguugaagucaaagcgugagcauug
guggauccaauacaagugagaaugccggcaugaguaacgcuugggaguga
gaaucucccaaaccgauugacuaagguuuccuggaccagggucguccuuc
caggguuagucuggaccuaagcugaggcugaaaagcguaggcgauggaca
acagguuaauauuccuguacuuacaguuagacugauggagugacaaagaa
gguuuuccacccccauaauuggauuuggggauaaaucauaaggugguaca
auaggcaaauccguugugcauaacauugagugaugaugucgagugaaagu
agcgaaggugguauuaaucaugcuuucaagaaaagcuucuaggguuaauc
uagcuguaaccaguaccgagaacgaacacacguagucaaggagaggaucc
uaagguuagcgagugaacuauagccaaggaacucugcaaauuaaccccgu
aaguuagcgagaaggggugcuuauguaaaaguaagccgcagugaagaacg
aggggggacuguuuaacuaaaacacaacucuaugccaaaccguaagguga
uguauauggggugacaccugcccagugcuggaagguuaaagaaggagguu
agcgcaagcgaagcuuuuaacugaagccccagugaacggcggccguaacu
auaacgguccuaagguagcgaaauuccuagucggguaaauuccgucccgc
uugaaugguguaaccaucucuugacugucucggcuauagacucggugaaa
uccagguacgggugaagacacccguuaggcgcaacgggacggaaagaccc
cgugaagcuuuacuguagcuuaauauugaucaggacauuaucauguagag
aauagguaggagcaaucgaugcaaguucgcuaggacuuguugaugcgaaa
gguggaauacuacccuugguugugugcuguucuaauugguaacuguuauc
caguuucaagacaguguuaggugggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcguacaaagguaccuucaguacgguuggaaaucg
uauguagaguguaaugguguaagggugcuugacugugagacauacagguc
gaacaggugagaaaucaggucauagugauccggugguccaguauggaaug
gccaucgcucaacggauaaaagcuacuccggggauaacaggcugauacug
cccaagaguucauaucgacggcaguguuuggcaccucgaugucgacucau
cucauccucgagcugaagcagguucgaaggguucggcuguucgccgauua
aagagauacgugaguuggguucaaaccgucgugagacagguuggucccua
ucuauugugcccguaggaagauugaagaguguugcuucuaguacgagagg
accgaagcgaggacaccucuuaugcuccaguuguagcgccagcugcaccg
cuggguaguaacgugucuauuagauaaacgcugaaagcaucuaaguguga
aacuaucucaaagauuaaucuucccauuucgcaagaaaguaagagccguc
aaagacgaugacguugauagguuacagguguaagcauagugauauguuga
gcugaguaauacuaauugcucgaggacu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pao Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 7.0 Å
• Binding residue (original residue number in PDB): S8 R9 S10 N11 S12 G13 I14 H15 Y22 N29 K30 K35 S36 V39 T40 K42 K43 H44 R47 N48 Q50 G51 K52 I53 T54 V55 R56 H57 Q58 G60 R61 K63 R64 K65 K72 Y88 P90 R92 A102 N103 G104 K106 H153 Q159 I160 A161 R162 S163 A164 S166 Y179 L184 L185 S186 E188 R190 L193 L206 H208 N209 V212 I213 G214 K215 G217 R218 N219 R220 H221 R222 R225 P226 T227 V228 R229 A232 M233 N234 H238 H240 E244 G245 R246 S247 P248 V249 R251 D252 T256 P257 W258 K260 H262 M263 G264 K266 T267 R268 K271 K272 R282
• Binding residue (residue number reindexed from 1): S7 R8 S9 N10 S11 G12 I13 H14 Y21 N28 K29 K34 S35 V38 T39 K41 K42 H43 R46 N47 Q49 G50 K51 I52 T53 V54 R55 H56 Q57 G59 R60 K62 R63 K64 K71 Y87 P89 R91 A101 N102 G103 K105 H152 Q158 I159 A160 R161 S162 A163 S165 Y178 L183 L184 S185 E187 R189 L192 L205 H207 N208 V211 I212 G213 K214 G216 R217 N218 R219 H220 R221 R224 P225 T226 V227 R228 A231 M232 N233 H237 H239 E243 G244 R245 S246 P247 V248 R250 D251 T255 P256 W257 K259 H261 M262 G263 K265 T266 R267 K270 K271 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:7pao, PDBe:7pao, PDBj:7pao
• PDBsum: 7pao
• PubMed: 36171285
• UniProt: P75577|RL2_MYCPN Large ribosomal subunit protein uL2 (Gene Name=rplB)