Structure of PDB 4v7w Chain DF Binding Site BS01

Receptor Information

>4v7w Chain DF (length=207) Species: 300852 (Thermus thermophilus HB8)

MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTAS
TKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYT
LPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDG
SESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWE
VFQNRIG

Ligand information

>4v7w Chain DA (length=2725)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccaagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcgccuacc
aaacccugucaaacuccgaagggucccagguggagccugggagugagggc
gcgagcgauaacguccgcguccgagcgcgggaacaaccgagaccgccagc
uaaggcccccaagucugggcuaagugguaaaggauguggcgccgcgaaga
cagccagucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucugggggaugaccccaggcgguaggggagcguucc
cgaugccgaugaaggccgacccgcgagggcggcuggagguaagggaagug
cgaaugccggcaugaguaacgauaaagagggugagaaucccucucgccgu
aagcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggac
cuaaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccg
gcccuucccgcaggugcgauggggggacgcucuaggcuagggggaccgga
gccauggacgagcccggccagaagcgcagggugggagguaggcaaauccg
ccucccaacaagcucugcgugguggggaagcccgcaaccccccgaagcca
gggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaa
accgacacaggugggcgggugcaagagcacucaggcgcgcgggagaaccc
ucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugc
ucccuggggugaugagccccggggagccgcagugaacaggcucuggcgac
uguuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggg
agcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccg
aaccgaagccccggugaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcgucaagccgguaaggacccgggaa
gaccacccgguggaugggccggggguguaagcgccgcgaggcguugagcc
gaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v7w Revisiting the structures of several antibiotics bound to the bacterial ribosome.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N29 H31 L32 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 T53 R54 G55 V57 A58 Y59 S60 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 A80 I82 F83 V84 V88 V89 F90 P92 R95 Y99 T100 L101 P102 K103 K104 R106 K107 G134 K135 T136 K137 R165 R168 N169 P171 E179 G180 N182 Y184
• Binding residue (residue number reindexed from 1): N29 H31 L32 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 T53 R54 G55 V57 A58 Y59 S60 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 A80 I82 F83 V84 V88 V89 F90 P92 R95 Y99 T100 L101 P102 K103 K104 R106 K107 G134 K135 T136 K137 R165 R168 N169 P171 E179 G180 N182 Y184

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:4v7w, PDBe:4v7w, PDBj:4v7w
• PDBsum: 4v7w
• PubMed: 20876130
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)