Structure of PDB 6gxn Chain C Binding Site BS01

Receptor Information

>6gxn Chain C (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>6gxn Chain A (length=2895)

guuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgaug
aaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguua
uaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuauc
auuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacauc
uaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcga
gcgaacggggagcagcccagagccugaaucaguguguguguuaguggaag
cgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaugc
acaugcugugagcucgaugaguagggcgggacacgugguauccugucuga
auauggggggaccauccuccaaggcuaaauacuccugacugaccgauagu
gaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggaguga
aaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggcg
ugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagc
aagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcg
uuaaguugcaggguauagacccgaaacccggugaucuagccaugggcagg
uugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaaa
aauuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggag
auagcugguucuccccgaaagcuauuuagguagcgccucgugaauucauc
uccggggguagagcacuguuucggcaaggggguacuuaccaacccgaugc
aaacugcgaauaccggagaauguuaucacgggagacacacggcgggugcu
aacguccgucgugaagagggaaacaacccagaccgccagcuaagguccca
aagucaugguuaagugggaaacgaugugggaaggcccagacagccaggau
guuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacuggu
cgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagc
ugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagcc
ugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcu
gacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaa
ggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggcg
aggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuugg
uguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguu
gucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauca
aggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugccc
ugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccca
aaccgacacagguggucagguagagaauaccaaggcgcuugagagaacuc
gggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgc
ugauauguaggugaggucccucgcggauggagcugaaaucagucgaagau
accagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacga
aaguggacguauacggugugacgccugcccggugccgggagguuaauuga
ugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaauggcguaaugauggccaggcugucuccacccgagacuc
agugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgga
aagaccccgugaaccuuuacuauagcuugacacugaacauugagccuuga
uguguaggauaggugggaggcuuugaaguguggacgccagucugcaugga
gccgaccuugaaauaccacccuuuaauguuugauguucuaacguugaccc
guaauccggguugcggacagugucugguggguaguuugacuggggcgguc
uccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucgg
acaucaggagguuagugcaauggcauaagccagcuugacugcgagcguga
cggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaau
ggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcug
auaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucg
gcucaucacauccuggggcugaaguaggucccaaggguauggcuguucgc
cauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgg
ucccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguac
gagaggaccggaguggacgcaucacugguguucggguugucaugccaaug
gcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaa
gcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccug
aaggaacguugaagacgacgacguugauaggccggguguguaagcgcagc
gaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gxn Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): K6 P7 T8 G11 R12 R13 H14 K17 K25 K27 E34 K35 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 R51 I53 G55 H57 K58 Y61 R62 I73 Y82 P84 N85 R86 L94 K96 D97 R100 G148 K149 Q152 L153 R155 S156 A157 T159 Y170 L175 R176 S177 E179 R181 A197 M200 V203 G205 K206 A207 G208 A210 R211 W212 R216 P217 T218 V219 R220 G221 T222 A223 M224 N225 P226 V227 D228 H229 G233 G234 E235 G236 R237 F239 G240 K241 H242 P243 W247 Q250 K252 G253 K254 K255 T256 R257 S258 K260 K264 R269 R270
• Binding residue (residue number reindexed from 1): K6 P7 T8 G11 R12 R13 H14 K17 K25 K27 E34 K35 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 R51 I53 G55 H57 K58 Y61 R62 I73 Y82 P84 N85 R86 L94 K96 D97 R100 G148 K149 Q152 L153 R155 S156 A157 T159 Y170 L175 R176 S177 E179 R181 A197 M200 V203 G205 K206 A207 G208 A210 R211 W212 R216 P217 T218 V219 R220 G221 T222 A223 M224 N225 P226 V227 D228 H229 G233 G234 E235 G236 R237 F239 G240 K241 H242 P243 W247 Q250 K252 G253 K254 K255 T256 R257 S258 K260 K264 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:6gxn, PDBe:6gxn, PDBj:6gxn
• PDBsum: 6gxn
• PubMed: 30076302
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)