Structure of PDB 1j5a Chain K Binding Site BS01

Receptor Information

>1j5a Chain K (length=197) Species: 1299 (Deinococcus radiodurans)

AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQV
SKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQ
LGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLV
TDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEE

Ligand information

>1j5a Chain A (length=2774)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaag
auucaaccccucaagccgaaguggcuggaaagcuacaccucagaagguga
gaguccuguaggcgaacgagcgguugacuguaaguaggucguuguucgug
aaacgaugacugaauccgcgcggaccaccgcgcaaggcuaaauacuccca
gugaccgauagcgcauaguaccgugagggaaaggugaaaagaaccccggg
aggggagugaaagagaaccugaaaccguggacuuacaagcagucauggca
ccuuaugcguguuauggcgugccuauugaagcaugagccggcgacuuaga
ccugacgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguc
cgaauagggcggcauuaguacgucgggcuagacucgaaaccaggugagcu
aagcaugaccagguugaaacccccgugacagggggcggaggaccgaaccg
gugccugcugaaacagucucggaugaguuguguuuaggagugaaaagcua
accgaaccuggagauagcuaguucuccccgaaauguauugagguacagcc
ucggauguugaccauguccuguagagcacucacaaggcuagccaaaccuu
augaaacuccgaaggggcacgcguuuaguccgggagugaggcugcgagag
cuaacuuccguagccgagagggaaacaacccagaccaucagcuaaggucc
cuaaaugaucgcucagugguuaaggaugugucgucgcauagacagccagg
agguuggcuuagaagcagccacccuucaaagagugcguaauagcucacug
gucgagugacgaugcgccgaaaaugaucggggcucaagugaucuaccgaa
gcuauggauucaacucgcgaagcgaguugucugguaggggagcguucagu
ccgcggagaagccauaccggaaggagugguggagccgacugaagugcgga
ugccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaagg
acaaggguuccuggggaagggucguccgcccagggaaagucgggaccuaa
ggugaggccgaacggcgcagccgauggacagcaggucaagauuccugcac
cgaucauguggagugauggagggacgcauuacgcuauccaaugccaagcu
auggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuac
cggucacaugccucagacguaucgggagcuuccucggaagcgaaguugga
aacgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccg
uaccgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcga
gagaacccucguuaaggaacuuugcaaucucaccccguaacuucggaaga
agggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacug
uuuaccaaaaucacagcacucugccaacacgaacaguggacguauagggu
gugacgccugcccggugccggaaggucaaguggagcggugcaagcugcga
aaugaagccccggugaacggcggccguaacuauaacgguccuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaaaggcguaacgaucu
gggcgcugucucaacgagggacucggugaaauugaauuggcuguaaagau
gcggccuacccguagcaggacgaaaagaccccguggagcuuuacuauagu
cuggcauugggauucggguuucucugcguaggugggagaaacuggccggu
cgguggccacccugagaaacuuggauuucuaaccugaaaaaucacuuucg
gggaccgugcuuggcggguaguuugacuggggcggucgccucccaaaaug
uaacggaggcgcccaaaggucaccucaagacgguuggaaaucgucuguag
agcgcaaagguagaagguggcuugacugcgagacugacacgucgagcagg
gaggaaacucgggcuuagugaaccggugguaccguguggaagggccaucg
aucaacggauaaaaguuaccccggggauaacaggcugaucucccccgaga
guccauaucggcggggagguuuggcaccucgaugucggcucgucgcaucc
uggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggc
acgcgagcuggguucagaacgucgugagacaguucggucucuauccgcua
cgggcgcaggagaauugaggggaguugcuccuaguacgagaggaccggag
ugaacggaccgcuggucucccugcugucguaccaacggcacaugcagggu
agcuauguccggaacggauaaccgcugaaagcaucuaagcgggaagccag
ccccaagaugaguucucccacuguucagguaagacucccggaagaccacc
ggguuaagaggccaggcgugcacgcauagcaauguguucagcggacuggu
gcucaucagucgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1j5a Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): T54 G63 N66 H69 F77 P86 P96 R159 L170 G174
• Binding residue (residue number reindexed from 1): T53 G62 N65 H68 F76 P85 P95 R158 L169 G173
• Binding affinity: PDBbind-CN: Kd=10nM

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:1j5a, PDBe:1j5a, PDBj:1j5a
• PDBsum: 1j5a
• PubMed: 11677599
• UniProt: Q9RXK1|RL4_DEIRA Large ribosomal subunit protein uL4 (Gene Name=rplD)