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Structure of PDB 4v8z Chain Ba Binding Site BS01

Receptor Information
>4v8z Chain Ba (length=148) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA
Ligand information
>4v8z Chain B5 (length=3147) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuaagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gacgaucaacuuagaacugguacggacaaggggaaucugacugucuaauu
aaaacauagcauugcgauggucagaaagugauguugacgcaaugugauuu
cugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggu
aaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguca
ucuaauuagugacgcgcaugaauggauuaacgagauucccacugucccua
ucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucag
cggggaaagaagacccuguugagcuugacucuaguuugacauugugaaga
gacguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacg
uucuagcauucaaggucccauucggggcugauccggguugaagacauugu
cagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcaga
uguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagg
guaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaag
uguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcca
gaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauagc
gacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu
........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<.<<<<<..<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>......
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<<...........<<<<<
<<.<<<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<....>>
>>>>.......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<
....>>>.....>>>>>>>....>>>>>>.>>>>>..<<<<........>
>>><<<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...
>>>...<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>
.<<<<<<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>
..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>
>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>
>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<
....<.<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<
....<<<....<<<<<..<<<<<<.....>>>>>>>>>>>....>>>..>
.>>.....>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>
>>>.>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<.
.....>>>...<<<<<<<..<<<<(((.....<<<<<<.....<<.....
.....<<<.<<<<<<<<<<..........<<<...<<.........>>..
.>>>.........<<......>>...........>>>>>>>>>>>>>...
.......))).>>...>>>>>>.>>>>..>>>>>>><<<<<<<<<.....
....>>>>>>>>>....>>>>>><.<<<<<<<<.<<......<<<<.<<<
<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.
....<<<<<<.......>>>>>><<<<<....<<<<<.<<...<<<<<<.
..<<.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>.
.......<<<<<<<.....>.>>>>>>....>>....>>...<<<<<...
.....>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<
<<...<<<<.<<<<<<<.<<<<<<<<<<..{{{..>>>>>><...<<<<<
....<<<<<<....<<<.....>>>....>>>>>>.....>>>>>....>
<<<<<<<......>>>>>>>>>>>...>>>>>>>.>>>>.........>>
>>>>..........>>>..>>>>>>>>>>>>..>>.....<<......>>
>>>>>.<<<<.....>>>>.>>>>>..<<<<.....<<<<<<<.<<....
...........<<<<<...............>>>>><<.<<<<<<<<<<<
..>>>>>..>>>>>>.>>............<<<<<<<<<..<<<......
...>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>.<.<<
..<<<..<<<<<<.<..<<<.....<<<<....>>>>.....>>>>>>>>
..>>>>><<<<<<.......>>>>>>........<...........<<<<
<.......>>>>>.....>.....>>.>..>>.>>>>>>>.....>>.>>
>>>>>..>>>>>>....>>....<<<<<........>>>>>....[[[[[
..{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<.
.......>>>>>>...<<<<<.....<<<<..<<<<<......>>>>>..
.............<<<<<......>>>>>..>>>>..>>>>>.....>>>
>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>>>
>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((
>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>
>>.>>))).......((((((..((((.>>>>>>))))))))))......
....]]]]..}}]]]].......<<.<...<<<<<<...<<.......>>
...>>>>>>....>.>.>.......<<<<<.<<<<<<..<.<<<<<<<..
....>>>>>>>...>.<<<.........>>>.....>>>>>..>...>>>
.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]....<<<
<<<<<..<<<<...<<<<<<...............>>>>>>..<<<<<..
.<<<<<...<<<<<<<<<<}}}.>>>>>..>>>>>..>>>>>..>>>>>.
<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>>>>>
>>.......<<<<<<.<<<.<<....<<..........<<<<<<.....>
>>>>>......>>.......<<<<<<...<<<<<.<..<<<......>>>
..>.>>>>>.>>>>>>.............>>.>>>.>>>>>>..<<<<<.
<.............>.....<<<<<<<<<.<<<....<<<<....<<<<<
......>>>>>...>>>>...>>>....>>>>.>>>>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v8z Molecular architecture of a eukaryotic translational initiation complex.
Resolution6.6 Å
Binding residue
(original residue number in PDB)		P2 S3 R4 F5 K7 T8 R9 K10 R12 G13 H14 V15 S16 A17 G18 K19 G20 R21 I22 H25 R26 K27 H28 P29 G30 G31 R32 G33 M34 A35 G36 H39 H40 H41 R42 I43 N44 K47 Y52 F53 G54 K55 G57 M58 R59 Y60 F61 H62 K63 Q64 H67 N74 K77 K111 L113 G114 K115 R117 S131 K132 L133 A149
Binding residue
(residue number reindexed from 1)		P1 S2 R3 F4 K6 T7 R8 K9 R11 G12 H13 V14 S15 A16 G17 K18 G19 R20 I21 H24 R25 K26 H27 P28 G29 G30 R31 G32 M33 A34 G35 H38 H39 H40 R41 I42 N43 K46 Y51 F52 G53 K54 G56 M57 R58 Y59 F60 H61 K62 Q63 H66 N73 K76 K110 L112 G113 K114 R116 S130 K131 L132 A148
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:0043232 intracellular non-membrane-bounded organelle
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4v8z, PDBe:4v8z, PDBj:4v8z
PDBsum4v8z
PubMed24200810
UniProtP02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)

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