Structure of PDB 8pv2 Chain Cd Binding Site BS01

Receptor Information

>8pv2 Chain Cd (length=462) Species: 759272 (Thermochaetoides thermophila DSM 1495)

GTGKKEKNRLLREGRTPGDPHVKGENFYRSAKKIKTLNILKEGKPIRDSK
GKIVKAASFQSKEVPKAVIEPNRKWFTNTRVISQDTLQSFREAMAEKQKD
PYTVLLKSNKLPMSLIRDGPKLEDGLKKHQAKMTIEREPFSETFGPKAQR
KRPKLSFNTVDELAGYSEQSLDSYHARLEEKKLLSVATAKEAIFNKGTSK
RIWNELYKVIDSSDVILHVLDARDPLGTRCRHVEKYLAAEAPHKHLVFVL
NKIDLVPSSQAAAWIRILQKDHPTCAMRASITNPFGRGSLIDLLRQFSVL
HKDRKQISVGLIGYPNVGKSSIINALRGKAVAKVAPIPGETKVWQYVTLM
KRIYLIDCPGIVPPNQHDTPEDLLLRGVVRVENVEHPEQYIPAVLRKVKQ
HHMERTYELRGWKDHIEFLEMLARKSGRLLKGGEPDVDGVAKQVLNDFMR
GKIPWFTPAPEP

Ligand information

>8pv2 Chain C1 (length=3056)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauagcag
ugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaa
gaagcccuuguuacuuaacugaacgugggcauucgaauguaucgacacua
gugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgc
gggguuaaggugccggaguggacgcucaucagacaccacaaaaggcguua
guacaucuugacagcaggacgguggccauggaagucggaauccgcuaagg
acuguguaacaacucaccugccgaauguacuagcccugaaaauggauggc
gcucaagcgucccacccauaccccgcccucaggguagaaacgaugcccug
aggaguaggcggccguggaggucagugacgaagccuagggcgugagcccg
ggucgaacggccucuagugcagaucuuggugguaguagcaaauacuucaa
ugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcgguu
ggacauggguuagucgauccuaagccauagggaaguuccguuucaaaggg
gcaugccccguguggcgaaagggaagccgguuaauauuccggcaccugga
uguggguuuugcgcggcaacgcaacugaacgcggagacgacggcgggggc
cccgggcagaguucucuuuucuucuuaacggucuaucacccuggaaacag
uuugucuggagauaggguuuaauggccggaagagcccgacacuucugucg
gguccggugcgcucucgacgucccuugaaaauccgcgggagggaauaauu
cucacgccaggucguacucauaaccgcagcagguccccaaggugaacagc
cucugguugauagaacaauguagauaagggaagucggcaaaauagauccg
uaacuucgggaaaaggauuggcucuaaggguugguaacaaccaacuuaga
acugguacggacagggggaaucugacugucuaauuaaaacauagcauugc
gauggccagaaagugguguugacgcaaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaa
cuaugacucucuguagccaaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaaaag
auuuuuuuacuuauucaaugaagcggggcuggacuugcguccaacuucug
gaguuaagguccuucgcgggccgacccggguugaagacauugucaggugg
ggaguuuggcuggggcggcacaucugugcagguguccuaaggggggcuca
uggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugauu
uugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccuu
uagucccucgaaauuugaggcuagaggugccagaaaaguuaccacaggga
uggcuuguggcggccaagcguucauagcgacgucgcuuugauccuucgau
gucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugaacucgucgcaaugguaauucagcuuagua
cgagaggaaccgcugauucagauaauugguuuuugcgguuguccgaccgg
gcagugccgcgaagcuaccaucugcuggauaauggcugaacgccucuaag
ucagaauccaugccagaacgcgacgauacuacccgcacguuguagacgua
uaagaauaggcuccggccucguauccuagcaggcgauuccuccgccggcc
ucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgcggga
ucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaagcagu
agaguagccuuguuguuacgaucugcugaggguaagcccuccuucgccua
gauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv2 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.63 Å
• Binding residue (original residue number in PDB): G2 T3 G4 K5 K6 E7 K8 R10 L11 G19 P21 H22 K24 E26 F28 Y29 R30 K33 I40 K42 R48 D49 S50 K75 T80 R81 Y103 K108 K129 A132 K148 Q150 K152 R153 A209 K216 T218 S219 K220 R221 I222 W223 N224 Y227 R251 H252 K255 Y256 A259 E260 L275 V276 P277 S278 T302 N303 R307 I311 R315 Q316 R324 K325 Q326 K349 V351 K353 P356 P358 G359 W364 Q365 Y366 V367 T368 K371 P384 N385 Q386 V398 R400 E402 N403 K419 H421 H422 S446 R448 L449 L450 K451 G452 Q463 R470 K472 F476 P478
• Binding residue (residue number reindexed from 1): G1 T2 G3 K4 K5 E6 K7 R9 L10 G18 P20 H21 K23 E25 F27 Y28 R29 K32 I39 K41 R47 D48 S49 K74 T79 R80 Y102 K107 K128 A131 K147 Q149 K151 R152 A189 K196 T198 S199 K200 R201 I202 W203 N204 Y207 R231 H232 K235 Y236 A239 E240 L255 V256 P257 S258 T282 N283 R287 I291 R295 Q296 R304 K305 Q306 K329 V331 K333 P336 P338 G339 W344 Q345 Y346 V347 T348 K351 P364 N365 Q366 V378 R380 E382 N383 K399 H401 H402 S426 R428 L429 L430 K431 G432 Q443 R450 K452 F456 P458

Gene Ontology

Molecular Function

• GO:0005525 GTP binding

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus

External links

• PDB: RCSB:8pv2, PDBe:8pv2, PDBj:8pv2
• PDBsum: 8pv2
• PubMed: 37921038
• UniProt: G0SBX1