Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 6vwl Chain M Binding Site BS02

Receptor Information
>6vwl Chain M (length=114) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAAST
VEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRV
QALADAAREAGLQF
Ligand information
>6vwl Chain 2 (length=2833) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggucggccug
cgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgac
gcuuaugcguuguuggguaggggagcguucuguaagccugcgaaggugug
cugugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaac
gauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccugucc
aacguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggc
guagucgaugggaaacagguuaauauuccuguacuugguguuacugcgaa
ggggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaa
gcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgu
gaugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaa
aagccucuaagcaucagguaacaucaaaucguaccccaaaccgacacagg
uggucagguagagaauaccaaggcgcuugagagaacucgggugaaggaac
uaggcaaaauggugccguaacuucgggagaaggcacgcugauauguaggu
gaggucccucgcggauggagcugaaaucagucgaagauaccagcuggcug
caacuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguau
acggugugacgccugcccggugccggaagguuaauugaugggguuagcgc
aagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
uggcguaaugauggccaggcugucuccacccgagacucagugaaauugaa
cucgcugugaagaugcaguguacccgcggcaagacggaaagaccccguga
accuuuacuauagcuugacacugaacauugagccuugauguguaggauag
gugggaggcuuugaaguguggacgccagucugcauggagccgaccuugaa
auaccacccuuuaauguuugauguucuaacguugacccguaauccggguu
gcggacagugucugguggguaguuugacuggggcggucuccuccuaaaga
guaacggaggagcacgaagguuggcuaauccuggucggacaucaggaggu
uagugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcag
gugcgaaagcaggucauagugauccggugguucugaauggaagggccauc
gcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaag
aguucauaucgacggcgguguuuggcaccucgaugucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcuguucgccauuuaaagugg
uacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugcc
gugggcgcuggagaacugaggggggcugcuccuaguacgagaggaccgga
guggacgcaucacugguguucggguugucaugccaauggcacugcccggu
agcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuug
ccccgagaugaguucucccugacccuuuaaggguccugaaggaacguuga
agacgacgacguugauaggccggguguguaagcgcagcgaugcguugagc
uaaccgguacuaaugaaccgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
..>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>..
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<.<<<<<<..<..>..>>>>
>>>>...........))).....>>>>>>.>>>...>>>>>>><<<<<<<
<<....>>>>>>>>>....>>>>>>..<<<<<...<<<......<<<<<<
<<....>>>>>>>>...>>>..>>>>>........>>>>>><......<<
.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<.
..<<.....>>.>>>>>>....((<<<.<<<...<<<...<<<....>>>
...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<<...
<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..
<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>
...>><..<<<<<....>>>>>...>>>>>>...>>>...>>>>......
...>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<......>>
>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<....
.....<.....<<<<<....<<..>>.....>>>>><<<<<<.....<<<
...<<<<.....>>>>...>>>...>>>>>>............<<<<<<<
<<..<<<.........>>>..<<<<<<<.....<<<....>>>.......
>>>>>>>.<<<<<.<<<..<<<<<<<..<<<....<...<<<....<<..
..>>.....>>>..>.....>>>>>>>>..>>>>>.<<<<<.......>>
>>>.........<...........<<<<<<.....>>>>>>.....>...
.>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>...
..<<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[[
<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<<...........<
<<<<...<<......<<<<<<<......>>>>>>>...>>..........
...>>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<<<.....>>>>>>
>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<......
.....>>>>>>.(<<...<<<<<<<...<<<<<<.......>>>>>>...
..<<)..(((>>....>>>>>>>...<<<<..<<<<....>>>>..>>>>
.<<<....>>>.>>))).......<<<<<<<.((..>>>>..))>>>>>>
>.............>>>>..]]>>>>.......<<<<...<<<<<<...<
<.......>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<
<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>
>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]..)))>>>
>>>>>....<<<<<<<...<<<<..<<<<<<<...............>>>
>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>..>>>>>..
.>>>>.>>>>>...<<<....<<<<<...........>>>>>....>>>.
>>>>.......>>>>>>>..<<<<<.....>>>>>.....<<..<<<<<.
......>>>>>....<<<<<<<<..<<....<<<<<....>>>>>...>>
...>>>>>.>>>.....>>.....>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vwl mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		R9 R10 R13 R16 L21 S91 R94 Q98 Y99 R111
Binding residue
(residue number reindexed from 1)		R6 R7 R10 R13 L18 S88 R91 Q95 Y96 R108
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vwl, PDBe:6vwl, PDBj:6vwl
PDBsum6vwl
PubMed32427100
UniProtP0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417