Structure of PDB 6wnt Chain b Binding Site BS01

Receptor Information

>6wnt Chain b (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>6wnt Chain 4 (length=3025)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggcugcuccccaugcgagaguaggga
acugccaggcauucggugccuggcggccguagcgcgguggucccaccuga
ccccaugccgaacucagaagugaaacgccguagcgccgaugguagugugg
gguaaaacgaugugggaaggcccagacagccaggauguuggcuuagaagc
agccaucauuuaaagaaagcguaauagcucacuggucgagucggccugcg
cggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgc
uuaugcguuguuggguaggggagcguucuguaagccugcgaaggugugcu
gugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaacga
uaaagcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaa
cguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggcgu
agucgaugggaaacagguuaauauuccuguacuugguguuacugcgaagg
ggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaagc
guguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcguga
ugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaaaa
gccucuaagcaucagguaacaucaaaucguaccccaaaccgacacaggug
gucagguagagaauaccaaggcgcuugagagaacucgggugaaggaacua
ggcaaaauggugccguaacuucgggagaaggcacgcugauauguagguga
ggucccucgcggauggagcugaaaucagucgaagauaccagcuggcugca
acuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguauac
ggugugacgccugcccggugccggaagguuaauugaugggguuagcgcaa
gcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaacgg
uccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaug
gcguaaugauggccaggcugucuccacccgagacucagugaaauugaacu
cgcugugaagaugcaguguacccgcggcaagacggaaagaccccgugaac
cuuuacuauagcuugacacugaacauugagccuugauguguaggauaggu
gggaggcuuugaaguguggacgccagucugcauggagccgaccuugaaau
accacccuuuaauguuugauguucuaacguugacccguaauccggguugc
ggacagugucugguggguaguuugacuggggcggucuccuccuaaagagu
aacggaggagcacgaagguuggcuaauccuggucggacaucaggagguua
gugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcaggu
gcgaaagcaggucauagugauccggugguucugaauggaagggccaucgc
ucaacggauaaaagguacuccggggaucugauaccgcccaagaguucaua
ucgacggcgguguuuggcaccucgaugucggcucaucacauccuggggcu
gaaguaggucccaaggguauggcuguucgccauuuaaagugguacgcgag
cuggguuuagaacgucgugagacaguucggucccuaucugccgugggcgc
uggagaacugaggggggcugcuccuaguacgagaggaccggaguggacgc
aucacugguguucggguugucaugccaauggcacugcccgguagcuaaau
gcggaagagauaagugcugaaagcaucuaagcacgaaacuugccccgaga
ugaguucucccugacccuuuaaggguccugaaggaacguugaagacgacg
acguugauaggccggguguguaagcgcagcgaugcguugagcuaaccggu
acuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wnt Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K6 P7 T8 P10 R12 R13 H14 K17 K25 K27 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 H52 G55 H57 K58 Q59 A60 Y61 R62 K70 I73 P84 R86 D97 G98 E99 R100 M145 K146 G148 K149 Q152 L153 A154 R155 S156 A157 G158 Y170 L175 R176 S177 E179 R181 E184 H199 M200 L204 G205 K206 A207 G208 R211 W212 R216 P217 T218 V219 R220 G221 T222 A223 M224 N225 V227 D228 H229 H231 G234 E235 G236 R237 N238 F239 G240 K241 H242 P243 V244 T245 P246 W247 Q250 T251 G253 K254 K255 T256 R257 K260 R261 T262 K264 R270
• Binding residue (residue number reindexed from 1): K6 P7 T8 P10 R12 R13 H14 K17 K25 K27 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 H52 G55 H57 K58 Q59 A60 Y61 R62 K70 I73 P84 R86 D97 G98 E99 R100 M145 K146 G148 K149 Q152 L153 A154 R155 S156 A157 G158 Y170 L175 R176 S177 E179 R181 E184 H199 M200 L204 G205 K206 A207 G208 R211 W212 R216 P217 T218 V219 R220 G221 T222 A223 M224 N225 V227 D228 H229 H231 G234 E235 G236 R237 N238 F239 G240 K241 H242 P243 V244 T245 P246 W247 Q250 T251 G253 K254 K255 T256 R257 K260 R261 T262 K264 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:6wnt, PDBe:6wnt, PDBj:6wnt
• PDBsum: 6wnt
• PubMed: 32518240
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)