Structure of PDB 4v85 Chain BD Binding Site BS01

Receptor Information

>4v85 Chain BD (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

Ligand information

>4v85 Chain BA (length=2853)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaaggggguccuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgaugugggaaggcccagacagccagga
uguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugg
ucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaag
cugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagc
cugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugc
ugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacca
aggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggc
gaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuug
guguuacugcgaaggggggacggagaaggcuauguuggccgggcgacggu
ugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauc
aaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcc
cugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccc
aaaccgacacagguggucagguagagaauaccaaggcgcuugagagaacu
cgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacg
cugauauguaggugaggucccucgcggauggagcugaaaucagucgaaga
uaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacg
aaaguggacguauacggugugacgccugcccggugccggaagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auggaaguguggacgccagucugcauggcuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v85 Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): M11 R13 Q36 N42 Y45 K56 R59 T61 K62 P63 E64 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 A119 K123 R124 N126 F127 R128 T129 Q130 A132 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 T171 Q173 S174 K190 G191 V193 P194 G195 A196 T197 K208
• Binding residue (residue number reindexed from 1): M11 R13 Q36 N42 Y45 K56 R59 T61 K62 P63 E64 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 A119 K123 R124 N126 F127 R128 T129 Q130 A132 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 T171 Q173 S174 K190 G191 V193 P194 G195 A196 T197 K208

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v85, PDBe:4v85, PDBj:4v85
• PDBsum: 4v85
• PubMed: 22187675
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)