Structure of PDB 4v4i Chain K Binding Site BS01

Receptor Information

>4v4i Chain K (length=137) Species: 262724 (Thermus thermophilus HB27)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDFGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAY

Ligand information

>4v4i Chain w (length=2889)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgucuaguccgcggccguggacccg
aaaccgggcgagcuagcccuggccagggugaagcuggggugagacccagu
ggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcua
ggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaauga
cuuuagggucagccucaggcgcugacuggggccuguagagcacugauagg
gcuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccc
agguggagccugggagugagggcgcgagcgauaacguccgcguccgagcg
cgggaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugg
uaaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagc
cauccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccg
aaaaugaucggggcucaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
agggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaa
agagggugagaaucccucucgccguaagcccaaggguuccuacgcaaugg
ucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagc
cgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggggg
gacgcucuaggcuagggggaccggagccauggacgagcccggccagaagc
gcagggugggagguaggcaaauccgccucccaaaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
uccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
gggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaac
ccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgc
cuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaa
auccgccggagagcgcaaggguagaagggggccugacugcgaggccugca
agccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugg
aagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugau
cucccccgagcguccacagcggcggggagguuuggcaccucgaugucggc
ucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccc
auuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgguc
ucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacga
gaggaccggaagggacgcaccucugguuucccagcugucccuccaggggc
auaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaag
cgggaagcccgccccaagaugaggccucccacggcgucaagccgguaagg
acccgggaagacgacccgguggaugggccggggguguaagcgccgcgagg
cguugagccgaccggucccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4i Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements
• Resolution: 3.71 Å
• Binding residue (original residue number in PDB): R6 K8 Y9 Q12 Q13 G15 R16 L17 K18 F29 Q45 Q46 A49 R56 H57 R67 F69 P70 D71 Y74 T75 K76 K77 V81 R82 M83 G84 K85 R101 I120 H123 K124 L125 P126 I127 K128 K130
• Binding residue (residue number reindexed from 1): R6 K8 Y9 Q12 Q13 G15 R16 L17 K18 F29 Q45 Q46 A49 R56 H57 R67 F69 P70 D71 Y74 T75 K76 K77 V81 R82 M83 G84 K85 R101 I120 H123 K124 L125 P126 I127 K128 K130

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:4v4i, PDBe:4v4i, PDBj:4v4i
• PDBsum: 4v4i
• PubMed: 16962654
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)