Structure of PDB 7uph Chain K Binding Site BS01

Receptor Information

>7uph Chain K (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>7uph Chain I (length=4438)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccag
ucaauaagucuugagcuaaccgguacuaaugaaccgugaggcuuaaccuu
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggauaacaggc
ugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugu
cggcucaucacauccuggggcugaaguaggucccaaggguauggcuguuc
gccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguuc
ggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagu
acgagaggaccggaguggacgcaucacugguguucggguugucaugccaa
uggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucu
aagcacgaaacuugccccgagaugaguucucccugacccuuuaagggucc
ugaaggaacguugaagacgacgacguugauaggccggguguguaaggacg
accuucgggagggcgcuuaccacuuugugauucaugacuggggugaaguc
guaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7uph Three-dimensional structure-guided evolution of a ribosome with tethered subunits.
• Resolution: 4.18 Å
• Binding residue (original residue number in PDB): P10 G11 R12 R13 H14 K17 H24 K25 G26 K27 P28 K35 K38 S39 R47 I48 H52 H57 K58 A60 Y61 R62 F66 E81 Y82 R86 K96 D97 G98 E99 M145 K146 P147 K149 Q152 L153 A154 R155 S156 A157 G158 L175 R176 S177 E179 R181 A197 H199 M200 V203 L204 G205 K206 A207 G208 W212 R216 T218 V219 R220 G221 M224 N225 V227 G233 G234 E235 R237 H242 W247 G253 K255 R257 R261 T262 R269 R270
• Binding residue (residue number reindexed from 1): P10 G11 R12 R13 H14 K17 H24 K25 G26 K27 P28 K35 K38 S39 R47 I48 H52 H57 K58 A60 Y61 R62 F66 E81 Y82 R86 K96 D97 G98 E99 M145 K146 P147 K149 Q152 L153 A154 R155 S156 A157 G158 L175 R176 S177 E179 R181 A197 H199 M200 V203 L204 G205 K206 A207 G208 W212 R216 T218 V219 R220 G221 M224 N225 V227 G233 G234 E235 R237 H242 W247 G253 K255 R257 R261 T262 R269 R270

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7uph, PDBe:7uph, PDBj:7uph
• PDBsum: 7uph
• PubMed: 35836020
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)