Structure of PDB 7bl5 Chain 9 Binding Site BS01

Receptor Information

>7bl5 Chain 9 (length=338) Species: 511145 (Escherichia coli str. K-12 substr. MG1655)

MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEAD
ENLNTLIDYRFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQG
TGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQKTNGTPGDKR
ELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGV
VRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRVLLHLIDIDPI
DGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI
AEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVV

Ligand information

>7bl5 Chain A (length=2913)

guuguaagguuaagcgacuaagcguacacgguggaugcccuggcagucag
aggcgaugaaggacgugcuaaucugcgauaagcgucgguaaggugauaug
aaccguuauaaccggcgauuuccgaauggggaaacccaguguguuucgac
acacuaucauuaacugaauccauagguuaaugaggcgaaccgggggaacu
gaaacaucuaaguaccccgaggaaaagaaaucaaccgagauucccccagu
agcggcgagcgaacggggagcagcccagagccugaaucaguguguguguu
aguggaagcgucuggaaaggcgcgcgauacagggugacagccccguacac
aaaaaugcacaugcugugagcucgaugaguagggcgggacacgugguauc
cugucugaauauggggggaccauccuccaaggcuaaauacuccugacuga
ccgauagugaaccaguaccgugagggaaaggcgaaaagaaccccggcgag
gggagugaaaaagaaccugaaaccguguacguacaagcagugggagcacg
cuuaggcgugugacugcguaccuuuuguauaaugggucagcgacuuauau
ucuguagcaagguuaaccgaauaggggagccgaagggaaaccgagucuua
acugggcguuaaguugcaggguauagacccgaaacccggugaucuagcca
ugggcagguugaagguuggguaacacuaacuggaggaccgaaccgacuaa
uguugaaaaauuagcggaugacuuguggcugggggugaaaggccaaucaa
accgggagauagcugguucuccccgaaagcuauuuagguagcgccucgug
aauucaucuccggggguagagcacuguuucggcaagggggucacuuacca
acccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacg
gcgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcu
aaggucccaaagucaugguuaagugggaaacgaugugggaaggcccagac
agccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauag
cucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaug
caccgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguu
cuguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagu
gcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccg
gaagaccaaggguuccuguccaacguuaaucggggcagggugagucgacc
ccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauucc
uguacuugguguuacugcgaaggggggacggagaaggcuauguuggccgg
gcgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaaucc
ggaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaa
caaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaau
cguaccccaaaccgacacagguggucagguagagaauaccaaggcgcuug
agagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggag
aaggcacgcugauauguaggugaggucccucgcggauggagcugaaauca
gucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugug
caaacacgaaaguggacguauacggugugacgccugcccggugccggaag
guuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccggua
aacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgg
guaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccac
ccgagacucagugaaauugaacucgcugugaagaugcaguguacccgcgg
caagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauu
gagccuugauguguaggauaggugggaggcuuugaaguguggacgccagu
cugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaa
cguugacccguaauccggguugcggacagugucugguggguaguuugacu
ggggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaau
ccuggucggacaucaggagguuagugcaauggcauaagccagcuugacug
cgagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggug
guucugaauggaagggccaucgcucaacggauaaaagguacuccggggau
aacaggcugauaccgcccaagaguucauaucgacggcgguguuuggcacc
ucgaugucggcucaucacauccuggggcugaaguaggucccaaggguaug
gcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugag
acaguucggucccuaucugccgugggcgcuggagaacugaggggggcugc
uccuaguacgagaggaccggaguggacgcaucacugguguucggguuguc
augccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaa
agcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuua
aggguccugaaggaacguugaagacgacgacguugauaggccgggugugu
aagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuua
accuuacaacgcc

<<<<<<<<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<
[[<<......<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..]
.>>>......>>>>>>>...>>>....<<<....>>><<<<<<<....>>
>>>>>.<<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....
<<....>>......>>>>>.>.........<<....>>..<<<<<<....
.<<.....>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<
.<<<...<<<<<......>>>>>((......<<<.....))>>>...>>>
...>>>>>>>>>>>>>...>>>>........<<<<<<<<.........>>
>>>>>>......<<<<<..<<<<>>>>>..)))......]].>>>>>>>.
]]...............<<....>>....]].........<<<<.....>
>>>.............}....>>>>>>>>>>>.......<<<<..<<<<<
......>>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<
<<<<<<<<..<<<...<<.....>>...>>>...<<....>>..<<<<..
...>>>>.....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<
<<<<..<<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<
<........>>>>>>>>....>>>>>>>>>...<<<.....>>>......
>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<
<...<<<<<<<<<.....<<<...<<<.<<<<...<<<<<<.>>>>.>>.
..>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<
<<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<.
..<<<(((.....<<<<<<...........<<..<<<<<..<<.......
.<<<<<......<<<<.......>>>>.............<<<......>
>>..>>>>>....>>..>>>>>.>>...........))).....>>>>>>
.>>>...>>>>>>><<<<<<.<<....>>.>>>>>>....>>>>>>..<<
<<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>..
......>>>>>><......<<.....<<<<<<.......>>>>>><<<<.
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<
<<...<<<...<<<....>>>...>>>...>>>..<<<<<........>>
>>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<
<....(((...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>
>>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>
>>...>>>...>>>>.........>>>>...>>....>>>>>>>>>>>.>
>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<
<<....<<<<<<<<.<<...............<<<<<.............
..>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<
<<....<...<<<<<<.<<....>>..>>>>>>..>.....>>>>>>>>.
.>>>>><<<<<.........>>>>>.....................<.<<
<.....>>>.>...........>>>>>..>>.>>>>>>>.....>>.>>>
>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<
<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<
<<<<.<<<<...........<<<<<...<<......<<<<<<<<....>>
>>>>>>...>>.............>>>>>..>>>>.>>>>>>>>>>>...
<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<
.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<
<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<
<..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<
<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>...
....<<<<....<<<<<...<<.......>>...>>>>>.....>>>.>.
......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<
<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>
>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<...<<<
<<<...............>>>>>>..<<<<<...<<<<...<<<<<<<<<
<<))).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...
........>>>>>....>>>.>>>>.......>>>>>>>..<<<<<....
.>>>>><....<<..<<<<<.......>>>>>....<<<<<<<<..<<..
..<<<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>
>>>>>>>>>>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bl5 Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): M1 R25 E26 K27 Y28 P30 K31 G32 G33 P34 E51 N52 I57 D58 R60 F61 R76 D77 C78 T79 K81 W122 H123 L125 R129 F130 K131 S132 S133 V134 R136 T137 A181 A182 Y189 F191 L198 V200 R202 A225 G226
• Binding residue (residue number reindexed from 1): M1 R25 E26 K27 Y28 P30 K31 G32 G33 P34 E51 N52 I57 D58 R60 F61 R76 D77 C78 T79 K81 W122 H123 L125 R129 F130 K131 S132 S133 V134 R136 T137 A181 A182 Y189 F191 L198 V200 R202 A225 G226

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0017111 ribonucleoside triphosphate phosphatase activity
• GO:0019003 GDP binding
• GO:0019843 rRNA binding
• GO:0032561 guanyl ribonucleotide binding
• GO:0043023 ribosomal large subunit binding
• GO:0046872 metal ion binding
• GO:0097216 guanosine tetraphosphate binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0007059 chromosome segregation
• GO:0022611 dormancy process
• GO:0042254 ribosome biogenesis
• GO:0042255 ribosome assembly
• GO:0090071 negative regulation of ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:7bl5, PDBe:7bl5, PDBj:7bl5
• PDBsum: 7bl5
• PubMed: 33639093
• UniProt: P42641|OBG_ECOLI GTPase ObgE/CgtA (Gene Name=obgE)