Structure of PDB 4v97 Chain DF Binding Site BS01

Receptor Information

>4v97 Chain DF (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

Ligand information

>4v97 Chain DA (length=2824)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucgcgaauccccag
ccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgua
ggcgaaagguggggggauaggugaggguacccgaguaccccgugguucgu
ggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacuccg
ggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaaccccg
ggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacgg
ccccgcaagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccagauagcucacuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaacaagcucugcgugguggggaagcc
cgggugacaaccccccgaagccagggagccaagaaaagccucuaagcaca
accugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagag
cacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccc
cguaacuucgggagaaggggugcucccuggggugaugagccccggggagc
cgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcg
aacucguaagaggagguauagggagcgacgcuugcccggugccggaaggu
caaggggaggggugcaagccccgaaccgaagccccggugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgg
ugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaa
gaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccug
cguaggauaggugggagccugugaacccccgccuccgggugggggggagg
cgccggugaaauaccacccuggcgcggcugggggccuaacccucggaugg
ggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaag
guaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgga
gagcgcaaggguagaagggggccugacugcgaggccugcaagccgagcag
gggcgaaagccgggccuagugaaccgguggucccguguggaagggccauc
gaucaacggauaaaaguuaccccggggauaacaggcugaucucccccgag
cguccacagcggcggggagguuuggcaccucgaugucggcucgucgcauc
cuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcgg
cacgcgagcuggguucagaacgucgugagacaguucggucucuauccgcc
acgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgga
agggacgcaccucugguuucccagcugucccuccaggggcauaagcuggg
uagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagccc
gccccaagaugaggccucccacggcgucaagccgguaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v97 Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
• Resolution: 3.516 Å
• Binding residue (original residue number in PDB): N29 H31 R38 L41 K43 R44 R45 R46 T48 A49 T51 K52 T53 R54 V57 A58 Y59 S60 R62 K63 Q67 K68 H69 R72 A73 R74 H75 P81 I82 F83 V84 G85 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 V105 R106 K135 T136 K137 R165 R168 N169 P171 E179 G180 N182 Y184 R205
• Binding residue (residue number reindexed from 1): N24 H26 R33 L36 K38 R39 R40 R41 T43 A44 T46 K47 T48 R49 V52 A53 Y54 S55 R57 K58 Q62 K63 H64 R67 A68 R69 H70 P76 I77 F78 V79 G80 V83 V84 F85 P87 R90 Y94 T95 P97 K98 K99 V100 R101 K130 T131 K132 R160 R163 N164 P166 E174 G175 N177 Y179 R200

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v97, PDBe:4v97, PDBj:4v97
• PDBsum: 4v97
• PubMed: 23630274
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)