Structure of PDB 4v4z Chain BD Binding Site BS02

Receptor Information

>4v4z Chain BD (length=272) Species: 300852 (Thermus thermophilus HB8)

KFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFR
GGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRY
IIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAK
LARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADHKNI
VLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWGWQT
KGLKTRKRRKPSSRFIIARRKK

Ligand information

>4v4z 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: 4v4z Structural basis for messenger RNA movement on the ribosome.
• Resolution: 4.51 Å
• Binding residue (original residue number in PDB): R13 F15 M16 T17 A19 I24 K38 K39 G42 R43 N44 N45 Q46 G47 R48 T50 V51 R52 F53 K59 R60 L61 F67 K68 W70 Y84 D85 P86 R88 V98 D99 G100 K102 P149 K150 K151 L155 A156 R157 A158 A159 G160 T161 Y172 L177 P178 S179 R183 H186 N198 A199 K202 L206 G207 K208 A209 G210 R211 R213 W214 L215 R218 H220 V221 R222 A225 M226 N227 V229 D230 H231 H233 G234 G235 E237 R239 A240 P241 R242 R244 P246 A247 S248 P249 W250 W252 Q253 T254 K255 G256 L257 T259 R260 R262 R263 K264 R268
• Binding residue (residue number reindexed from 1): R9 F11 M12 T13 A15 I20 K34 K35 G38 R39 N40 N41 Q42 G43 R44 T46 V47 R48 F49 K55 R56 L57 F63 K64 W66 Y80 D81 P82 R84 V94 D95 G96 K98 P145 K146 K147 L151 A152 R153 A154 A155 G156 T157 Y168 L173 P174 S175 R179 H182 N194 A195 K198 L202 G203 K204 A205 G206 R207 R209 W210 L211 R214 H216 V217 R218 A221 M222 N223 V225 D226 H227 H229 G230 G231 E233 R235 A236 P237 R238 R240 P242 A243 S244 P245 W246 W248 Q249 T250 K251 G252 L253 T255 R256 R258 R259 K260 R264

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v4z, PDBe:4v4z, PDBj:4v4z
• PDBsum: 4v4z
• PubMed: 17051149
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)