Structure of PDB 6zxf Chain z Binding Site BS01

Receptor Information
>6zxf Chain z (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDSVINKVTEKSRQKEADMYRIKDKADRATVEQVLDPRTRMILFKMLTRG
IITEINGCISTGKEANVYHASTANGESRAIKIYKTSILVFKDRDKYVSGE
FRFRHGYCKGNPRKMVKTWAEKEMRNLIRLNTAEIPCPEPIMLRSHVLVM
SFIGKDDMPAPLLKNVQLSESKARELYLQVIQYMRRMYQDARLVHADLSE
FNMLYHGGGVYIIDVSQSVEHDHPHALEFLRKDCANVNDFFMRHSVAVMT
VRELFEFVTDPSITHENMDAYLSKAMEIASQRTKSSQDHVDEEVFKRAYI
PRTLNEVKNYERDMDIIMKLQDNILYQTVTGLKKDLSGVQKVPAKKERKK
MVKEAQREKRKNKIPKHVKKRKE
Ligand information
>6zxf Chain 2 (length=1656) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggcuacagugaaacugcgaauggcucauuaa
aucaguuaugguuccuuuggucgcucguacuuggauaacugugguaauuc
uagagcuaauacaugccgacgggcgcugacccccuucgcgggggggaugc
gugcauuuaucaguggugacucuagauaaccucgggccgaucgcacgcgc
ggcgacgacccauucgaacgucugcccuaucaacuuucgaugguagucgc
cgugccuaccauggugaccacgggugacggggaaucaggguucgauuccg
gagagggagccugagaaacggcuaccacauccaaggaaggcagcaggcgc
gcaaauuacccacucccgacccggggagguagugacgaaaaauaacaaua
caggacucuuucgaggcccuguaauuggaaugaguccacuuuaaauccuu
uaacgaggauccauuggagggcaagucuggugccagcagccgcgguaauu
ccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcucguagu
uggaucucucucggccgaagcguuuacuuugaaaaaauuagaguguucaa
agcaggccgccuggauaccgcagcuaggaauaauggaauaggaccgcggu
ucucggaacugaggccaugauuaagagggacggccgggggcauucguauu
gcgccgcuagaggugaaauucuuggaccggcgcaagacggaccagagcga
aagcauuugccaagaauguuuucauuaaucaagaacgaaagucggagguu
cgaagacgaucagauaccgucguaguuccgaccauaaacgaugccgaccg
gcgaugcggcggcguuauaugacccgccgggcagcuuccgggaaaccaaa
gucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaa
uugacggaagggcaccaccaggaguggagccugcggcuuaauuugacuca
acacgggaaaccucacccggcccggacacggacaggauugacagauugau
agcucuuucucgauuccgugggugguggugcauggccguucuuaguuggu
ggagcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcu
aacuaguuacgcgacccccggucggcguaacuucuuagagggacaagugg
cguucagccacccgagauugagcaauaacaggucugugaugcccuuagau
guccggggcugcacgcgcgcuacacugacuggcucagcgugugccuaccc
uacgccggcaggcgcggguaacccguugaaccccauucgugauggggauc
ggggauugcaauuauuccccaugaacgaggaauucccaguaagugcgggu
cauaagcuugcguugauuaagucccugcccuuuguacacaccgcccgucg
cuacuaccgauuggaugguuuagugaggcccucggaucggccccgccggg
gugcccuggcggagcgcugagaagacggucgaacuugacuaucuagagga
aguaaaagucguaacaagguuuccguaggugaaccugcggaaggaucauu
aacgga
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<.......>>...>>.>>......<<......
..<<<.<....<<....<<<<..........<<.....<<.<<<.....>
>>.>>......>>.........<<<<...<<<..........>>>...>>
>><<..<<<<<...<......>..>>>>>......>>...<<<<.<<..>
>>>>>..>.>>>...>>..>.>>>.<<<....<<<....<<<<<<<....
.....>>>>>>>>>>......>>>...<<<.<<<<....>>>>....>>>
.>>.<<.<<<..........>>>.>>.<.<<....>>.>...>>>>>>..
.......<<<....<<<<...>>>>..>>>..>...>>.>.....<<<<<
<<<<.<<<....>>>..>>>>>>.>>>......<<..<...........>
..>>.........<<<<<((......<<<<.....<<..))>>.......
>>>>.>>>>>..>>>>>>.>>>.........<.<((.....<.<<...<<
<.<<...<<.<<<..>>>>>...<<<<<<.<.......<<...<......
.>.<<<<.>>>>...>>......>.>>>..>>>........<.<<.<<<<
<<...>>>>>>.>>.>....>>....<<<<<<..<...<<<<..<<..<<
<<<<<<...<<<......>>>......>>>>>>>>..>>.......<<..
..>>...>>>>..>..>>>.>>>...>>>...>>.>....<<<<<<<...
<...<<<<.........>>>>...>>>>>>>>..........<<<.<<.<
<<..<.<<<<<<.<<<<<>>>>>>>>>>>.>..>>>...<<..))>>...
>>.....>>>.>.>.<<<......<<<<....>>>>....>>>..)))).
]<<<<<.<<<<<<<..<<..<<<<<..<<<.<<<<<<......<<.....
...>>..........<<<<<.<....<<<<<<.......<<.<<<.....
...>>>.>>.....>>>>>>.<.<<.<<<..<<.<<<<<<....<<<.<<
<<......>>...<<<......>>>...>>.>>>....<<<...<...<<
<<..<<<<<<<<<<<<...>>>>.>>>>>>>>..>>>>..>.....<<<<
<.....>>>>>........>>>....>>>.>>>.....>>>>>>>>....
>.>>>>>...>>.>>>>.>>>.....<<.<<<........<.......<<
<.<<<<....>>>>.>>>....>.........>>>.>>.........<<.
<<<<<..........>>>>>>>.........>>>>>.....<<<<<<<<.
......>>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<.
.<<<<.<<.....<<<<<<<.<<<..<<<<.<<...<<<<<<<<<<.<<<
<..>>>>.>>>>.>.>>>>>...>>.>>>>..>>>.>>>>>>>....>>.
>>>>...>.>>...>.....<<<<<<<<<....>>>>>>>>>........
......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6zxf Structural basis for the final steps of human 40S ribosome maturation.
Resolution3.7 Å
Binding residue
(original residue number in PDB)
D129 N133 E137 R140 R148 K150 K152 R155 A156 T157 V158 T188 K190 F217 K222 F228 R229 H232 G233 C235 N238 R240 K241 E248 R252 I255 R271 F328 D349 N363 K535 K536 V538 K539 R543 K545 R546 K549 P551 K552 K556 R557 K558
Binding residue
(residue number reindexed from 1)
D2 N6 E10 R13 R21 K23 K25 R28 A29 T30 V31 T61 K63 F90 K95 F101 R102 H105 G106 C108 N111 R113 K114 E121 R125 I128 R144 F201 D222 N236 K349 K350 V352 K353 R357 K359 R360 K363 P365 K366 K370 R371 K372
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
3.6.3.-
Gene Ontology
Molecular Function
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0016310 phosphorylation
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:2000234 positive regulation of rRNA processing
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030688 preribosome, small subunit precursor
GO:0034708 methyltransferase complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6zxf, PDBe:6zxf, PDBj:6zxf
PDBsum6zxf
PubMed33208940
UniProtQ9BRS2|RIOK1_HUMAN Serine/threonine-protein kinase RIO1 (Gene Name=RIOK1)

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