Structure of PDB 4w2e Chain y Binding Site BS01

Receptor Information

>4w2e Chain y (length=644) Species: 300852 (Thermus thermophilus HB8)

MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEAR
IRAQAKRLAERKAEAERLKEILENLSRIRNFSIIAHVDHGKSTLADRILE
LTHSAVRVTYRAKDGEEYVFHLIDTPGHVDFTYEVSRALAAVEGVLLVVD
ASQGVEAETLAKFYMALEHGHVIIPVINKIDLPNARPLEVALEVEEVLGL
PADEAIFASGKTGEGVEEILEAIVQRIPPPKGDPEAPLKALIFDSVYDAY
QGVIPYLRLFEGRVRPGDRIRIYSTGKEFTVDKVGVFTPQGLVATEALEA
GEVGWLVAAIRDIHDVQVGDTITLADRPTPSPYPGFRPAKPVVFAGLYPV
DSGDYGKLRDALEKLKLNDAALTFEPESSTALGFGFRCGFLGLLHAEIVQ
ERLEREFGLSLIATAPSVVYKVRLKSGEEVEVHNPADLPDPTRIEEILEP
YVKLTIFTPEEYVGSLMQLLQEKRGRLVNMNYLPGAQKRVELVYEAPFAE
ILYDFHDRLKSVSRGYASMDYEQAGYRPGDLVKVNVLVHGEVVDALTFIA
HREKAYTMARAIVDKLAEVIPRQLFEVPIQAAIGGKIIARATVKALRKDV
LAKCYGGDVTRKKKLLEKQKEGKKRLKAIGKVEVPQEAFLAVLS

Ligand information

>4w2e Chain A (length=2873)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcagggguuguggcgugccuauugaagcaugagccggcgacuc
acggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccga
guccgaacagggcgcaagcggccgcaaaguccgcggccguggacccgaaa
ccgggcgagcuagcccuggccagggugaagcuggggugagacccagugga
ggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagga
gugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuu
uagggucagccucaggcgcugacuggggccuguagagcacugauagggcu
agggggcccaccagccuaccaaacccugucaaacuccgaagggucccagg
uggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcgg
gaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaa
aggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccgggugacaaccccccgaagccagggagccaagaaaagccucuaag
cacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugca
agagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguug
gccccguaacuucgggagaaggggugcucccuggggugaugagccccggg
gagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucuc
ugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgga
aggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggac
ccggugaaauugaacuggccgugaagaugcggccuacccguggcaggacg
aaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcg
ccugcguaggauaggugggagccugugaacccccgccuccgggugggggg
gaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucgg
auggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccua
aaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgc
cggagagcgcaaggguagaagggggccugacugcgaggccugcaagccga
gcaggggcgaaagccgggccuagugaaccgguggucccguguggaagggc
caucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccc
cgagcguccacagcggcggggagguuuggcaccucgaugucggcucgucg
cauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaa
gcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauc
cgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggac
cggaagggacgcaccucugguuucccagcugucccuccaggggcauaagc
uggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaa
gcccgccccaagaugaggccucccacggcagccgguaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4w2e Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): H17 E114 G422 Q426 Q429 E430 D465 K468 R472 G473 R555 D557 K561 C562 Y563 R569 K570 K576 G580 K581 R583
• Binding residue (residue number reindexed from 1): H86 E156 G464 Q468 Q471 E472 D507 K510 R514 G515 R597 D599 K603 C604 Y605 R611 K612 K618 G622 K623 R625

Enzymatic activity

• Catalytic site (original residue number in PDB): K22 S23 H86
• Catalytic site (residue number reindexed from 1): K91 S92 H128
• Enzyme Commision number:
  3.6.5.n1: elongation factor 4.

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0043022 ribosome binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0045727 positive regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0005886 plasma membrane

External links

• PDB: RCSB:4w2e, PDBe:4w2e, PDBj:4w2e
• PDBsum: 4w2e
• PubMed: 25104389
• UniProt: Q5SKA7|LEPA_THET8 Elongation factor 4 (Gene Name=lepA);
  Q5SLQ1|RL9_THET8 Large ribosomal subunit protein bL9 (Gene Name=rplI)