Structure of PDB 4v4y Chain BE Binding Site BS01

Receptor Information

>4v4y Chain BE (length=206) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKAAK

Ligand information

>4v4y Chain BA (length=2889)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
gggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaac
ccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgc
cuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaa
auccgccggagagcgcaaggguagaagggggccugacugcgaggccugca
agccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugg
aagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugau
cucccccgagcguccacagcggcggggagguuuggcaccucgaugucggc
ucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccc
auuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgguc
ucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacga
gaggaccggaagggacgcaccucugguuucccagcugucccuccaggggc
auaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaag
cgggaagcccgccccaagaugaggccucccacggcgucaagccgguaagg
acccgggaagaccacccgguggaugggccggggguguaagcgccgcgagg
cguugagccgaccggucccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4y Structural basis for messenger RNA movement on the ribosome.
• Resolution: 5.5 Å
• Binding residue (original residue number in PDB): G10 M11 T12 R19 V21 R36 E40 K41 V47 P56 K57 V59 N60 R61 K64 G65 L78 R79 I81 K109 G110 R111 F113 A114 G115 M117 W120 N121 F122 A123 D127 S128 H129 A131 H132 K133 I134 H135 R136 P138 G139 S140 I141 G142 N143 R144 K145 T146 R149 V150 Y151 K152 G153 M156 H159 Y160 A162 R164 V165 T166 M168 N169 K185 A187 V188 G190 P191 N192 K203 A204 A205 K206
• Binding residue (residue number reindexed from 1): G10 M11 T12 R19 V21 R36 E40 K41 V47 P56 K57 V59 N60 R61 K64 G65 L78 R79 I81 K109 G110 R111 F113 A114 G115 M117 W120 N121 F122 A123 D127 S128 H129 A131 H132 K133 I134 H135 R136 P138 G139 S140 I141 G142 N143 R144 K145 T146 R149 V150 Y151 K152 G153 M156 H159 Y160 A162 R164 V165 T166 M168 N169 K185 A187 V188 G190 P191 N192 K203 A204 A205 K206

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v4y, PDBe:4v4y, PDBj:4v4y
• PDBsum: 4v4y
• PubMed: 17051149
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)